When 2e first came out, there were no kits, all classes but fighter, mage, cleric, and thief were optional, and proficiencies were optional. But every source assumed you aren't limited to those four classes. Every source seemed to assume you were playing with proficiencies. And as soon as kits came into being, you had entire books essentially devoted to coming up with new kits.
Fast forward a few. Now we have 3e. Prestige classes were optional. Anyone checked the content of Complete Anything recently?
I'm not saying that I dislike prestiege classes or kits, I actually liked 2e's non-weapon proficiencies, and I certainly wouldn't try limiting PCs to four classes. But did any of those turn out to actually be optional? It seems to me that the moment you introduce a rule, it becomes part of the system. Perhaps because min-maxers see some way to break it. Perhaps the DM or a publisher thinks of a cool way to integrate it into the design. My point with all this being: modules. In 5e, will they really be optional?
You're entirely correct in noting that, in most editions and sourcebooks, later material assumes you're using earlier material, and that perhaps optional things shouldn't be supported, in order for people who don't use them to not feel left out or have space taken up in generic books with material for modules they don't use.
Flip that around for a second, and look at the later 3e books. Tome of Magic and Tome of Battle were quite popular among the fanbase, but new binding and shadowcasting material only showed up in web enhancements, and new ToB material didn't show up at all. Incarnum and warlocks got a few pages in Dragon Magic, but that's it. The wu jen and shugenja, nice fluffy elemental casters, didn't even get an official expanded spell list, just a suggestion in the foreword of Spell Compendium that you use your best judgment when picking out thematic spells for them because the designers couldn't be bothered. Teamwork benefits, something that every party should be clamoring for, showed up in a handful of books. Complete Champion only focused on Greyhawk religions--and only the core ones, even though many other Greyhawk gods were presented in Complete Divine. And how many books had skill tricks in them, again?
In contrast, every new book had cleric, wizard, and druid spells. Every new book had items, feats, or other perks relating to sneak attack. Sometimes it feels like there are more monk fighting styles, paladin variants, and caster ACFs than there are elf or dwarf subraces. The core material gets supported everywhere, while the scout cowers in the shadow of the ranger and rogue and the ninja resents the monk for his screen time.
It is in fact that very philosophy of "Assume everyone has core, don't support anything else" that lasted for so long before the devs wised up that led to many of 3e's problems. There are over 2000 spells in 3e, so yes, as far as your wizard is concerned, you
can have a spell for anything...while the supposed king of blasting, the warmage, pales in comparison because he only has material from 2 books, the PHB and his own. Skill tricks and expanded skill uses (subsystems that would let rogues and other skilled classes take advantage of their tons of skill points and possibly attempt to catch up to casters in the utility department) and teamwork benefits and command benefits (subsystems that would let marshals, fighters, and other leader-y classes (A) mechanically support their theme and (B) contribute better to the team) showed up in a handful of books and disappeared.
You see the same thing in 4e, though to a lesser extent. Runepriests vs. clerics, avengers vs. paladins, psions vs. wizards...early material will always have more support than later material simply by virtue of being first, and if you deliberately choose not to support later material it widens the gap, making the new material less appealing and making it narrower and weaker for those people who want to use it anyway.
So no, modules should not be "optional" in the sense that they are assumed not to exist in later books. Either every book should have NWPs or PrCs or themes or the like, or specific "The Complete Guide to Proficiencies" or "Ultimate Prestige" sourcebooks should be released supporting them, even if doing so takes time and effort away from supporting core options.