The details of your example are scant, but it would appear you were in some sense unaware of threats being present or, at least, threats to your owl.
Indeed, it was a dark forest, at night, and I was LOOKING for threats, with a creature supremely suited for that. Do you call that taking risks ?
Is it reasonable in the context of that campaign setting that monsters like kobolds hunt creatures like owls for sustenance or for their feathers, etc.?
It's exactly like the stormwind fallacy, a DM, like a player, can always find a reason to kill a familiar if he is looking for it, usually by inventing something justification that was not there 10 seconds ago. This is exactly the problem of the "kill familiar on sight" DM, he will let you play a familiar, but will invent any sort of excuse to do it as soon as they can (and being a DM, they can very easily do that).
I much prefer a DM telling me "I don't allow familiars" than a DM doing the above, much less frustration involved.
Was the owl keeping watch for threats so that it's PP applied to noticing the kobolds?
Once more, you don't have to watch for threats to have PP apply. And by default, in D&D, everyone is watching for threats, all the time. The PH tells you it straight up. Please don't bring up that one sentence that means something else entirely than what you think it means, this was not travelling and the owl was certainly not bent over a table making a map.
Moreover, since the owl was LOOKING FOR THREATS, I dare say that it was.
Was the owl hiding? If so, did you make a Stealth check and failed compared to the kobold's PP? Or, alternatively, did the DM make a Stealth check to resolve the kobolds getting the drop on the owl? Was the owl surprised? Did the owl lose initiative? Or did the familiar just die without any of those things taking place? Because if that's what happened, then that definitely seems unfair to me!
The owl was flying as discreetly as it could, at night, with a darkvision, stealth and senses far superior to kobolds. But then it just died.
"At risk" means that you put them in harm's way. If you don't want them targeted, don't do that. If you want advantage on your attack via the Help action, know that your familiar is now a target. If they're flying around spewing fire, a monster might loose an arrow at them or throw a rock. They might even ready an attack to do it.
And if I see them readying an attack instead of attacking, I will probably do something else that turn. But with a familiar with flight and flyby, is it really taking a risk ? That's where the problem is, it shouldn't be.
Failure to telegraph threats sets up situations where attacks or traps can be perceived by players as a "gotcha."
And putting everything in the open reduces the game to a boardgame where everything is on the table and you just need to compute probabilities. There is no reason nor requirement for a DM to telegraph threats or make them explicit. The discovery and investigation, and surprise, is part of the game too, actually a more interesting part for some of us than crunching numbers in combat.
Does a monster need to know the owl flapping around their heads, making it easier for an adventurer to hit them, is a familiar in order to target them? No.
And of course, it's more important to target the owl because of the standing "kill familiar on sight" order than the fighter in your face, the rogue in the shadows and the wizard peppering you with magic missiles...
Look I have nothing against adversaries targeting familiars if the player abuses them by always claiming advantage and invulnerability, but this is not what we are speaking of, a "kill familiar on sight" is just a reason to aggravate players who just want a scout under reasonable conditions, and who expect a well chosen familiar to be sufficiently discrete or blending in to not be hunted and killed on sight. There are rats in the sewers. There are ravens flying over the streets during the day, there are owls flying at night in the wood. Are these all killed on sight just because they might be familiars ? Or are just familiar targeted because they are an annoying player feature ?