The wizards (Varthlokkur, Mist, and the Star-Rider) are not omnipotent or omniscient. They don't know everything. In fact, their knowledge is sometimes stunningly specific. They don't have time to see everything. They often let things go, assuming they can just deal with the consequences later. They are petty. They have human concerns.
Reminds me of the well-written wizards in The Forgotten Realm's The War of the Spider Queen series (contrast with some Mary Sue wizards in the same setting).
There are multiple intrigues at multiple levels in multiple directions. Assuming a wizard can handle "X" number of intrigues ( for instance, equal to his INT score), he's got to allocate a goodly portion of those to minding intrigues targeting him, not just ones he's set in motion, lest he be ambushed.
I'm not too familiar with Cook's setting. Assuming you're talking about wizards in any setting, and not just Cook's, I would assume that different wizards would have different ways of dealing with these issues (and some would have none).
Adventuring wizards (and those working for the military) always have backup. Furthermore no one is likely angry at
just the wizard, but at the whole party. Of course, the party can't be together all the time, and said wizard might fear being ambushed while having a bath, but their risk is only a bit worse than if a tougher PC were ambushed while having a bath.
Since in most settings wizards are rare, each military wizard of high enough level/notability would probably have a small staff, dealing with administration issues at the very least. Most likely said wizard would feel they don't have enough support though, but at least they've got someone to buy scrolls, ritual components and what not for them. They also spend time at the officer's barracks, which are well-guarded, and if the military is at all suspicious of them, some low-ranking beneath notice soldiers might follow them around and have to rescue them if someone attacks said wizard.
Mercenary wizards would probably have it worse, especially if they're essentially adventuring wizards without a permanent party, hiring themselves out for temporary jobs. No backup, no administration most of the time. The good news if anyone going after them is really angry at their paymaster instead of them, and is probably more interested in what information they hold in their heads rather than in killing them for revenge. Being a "standup mage" would enhance their reputation, but could result in torture rather than just being threatened.
Solitary wizards who aren't interested in anything beyond magic would be able to evade most threats simply by hiding in a well-trapped tower. Their greatest concerns would probably be theft ("thieves" might want to steal their items, ritual scrolls, etc) or if they had past lives as adventurers, they might have old enemies with scores to settle. Said wizards might have a mage-only staff consisting solely of apprentices, who are there to do lesser work the wizard just doesn't have time for. Said wizards would likely rely on powerful intimidating constructs for physical protection.
I think few wizards would actually be interested in intrigue. Those that are noble (or at least work for a noble house), work for the government or for criminal guilds might really be constantly deep into intrigue. They're no longer "magic first", they're "country first", "family first" or even "me first". Said wizards would have special skills in dealing with intrigues, and would constantly be on guard (even paranoid), slathering themselves with protective wards and contingencies and always having escape spells prepped.
As said wizards are becoming paranoid, they might find it hard to hire help or bodyguards. Assuming they're not worried about being stabbed in the back at any moment, they might have to hide things from these employees (and so be alone a lot) because they fear old-fashioned espionage.
Really powerful wizards (eg the Minister of Magic, the Minister of Espionage) might frequently subject their staff to lie-detection or mind-reading magic, which isn't exactly a great way of maintaining trust.
Fortunately, if these wizards are powerful enough, they could create anything from golems to undead servitors to protect them. (Their own bosses, if they have any, might insist they maintain staff sent from the palace.) The more paranoid wizards might create semi-independent creatures, intelligent enough to observe things the wizard themselves might miss, but generally loyal to the wizard. (Not quite a wizard example, but it gets the point across: in War of the Spider Queen, Triel carried an intelligent snake-headed whip which made observations for her, seeming in 4e terms to give her a bonus to Insight and Perception, and crucially kept watch for her even as she slept. However, the whip couldn't cast spells or do more than warn her of things.)
The exact amount of preparation required would depend on the ruleset. Until very high levels, a Contingency/Teleport by itself would deal with most ambushes, even if the wizard is caught by surprise by an entire party. I would expect any 3.x wizard, even if not in the least bit interested in combat, to always have a few defensive spells, if only because a wizard who isn't dressed or otherwise identified as one runs the risk of being mugged. Spells that take you far from combat (eg Dimension Door) are probably better than ones that don't (eg Stoneskin) since combat defensive spells (other than perhaps Invisibility) can be surmounted by determined-enough foes.
A very high level wizard might have to go paranoid, always changing traps on the various vulnerable areas of their homes or hangouts (doors, bathroom, kitchen table), buying gorgon's blood to perform the Forbiddance ritual (that's not actually in the rules, but IIRC gorgon's blood blocked scrying in 3.x much like Forbiddance), and (if in 3.x) layering themselves with spells like Foresight to avoid ambushes or (if in 4e) preparing the Succor ritual to immediately teleport to a pre-determined location if ambushed (and conscious enough to escape).
The last example is the worst of both worlds - liches. A lich might have a huge ego, and they're not comforting to living staff. A wizard willing to do that to themselves might have been mad to begin with, and more likely afterward. Liches, being generally actively evil, probably aren't just hiding in a cave in the Underdark working on research, although they "live" so long they might outlive anyone actively seeking them out. A more "out-going" lich might use magic disguises to visit the world of the living, hire a majordomo or chief of staff and otherwise meddle, increasing both their non-magical knowledge and risk of uncovery. Said lich probably has a fairly time-specific goal.
TL;DR:
I think "intrigue" is a skill, and many wizards would not possess it. These wizards would either avoid jobs where they need this skill, or they'd fail pretty quickly at it. Especially in an RPG it's probably pretty hard to find a wizard whose Int isn't, in the long-run, just based on their level. A higher-level wizard is smarter, so naturally they can deal with more intrigues.