Because missile launcher (and magazine) performance does not improve drastically after about tech cost 15k (possibly 30k), I find it easier to standardize launchers and magazines (total loadouts, launcher fire rate and size, etc.) earlier in the game than any other tech-dependent component. This makes it easy to "pick sizes, and stick with them", which in turn reduces micromanagement and waste in ship design, missile design, ship building, missile manufacturing, and so forth.
Nor does sticking with standard sizes necessarily lock you into one mode of missile combat. You can easily both supply shorter-range, harder-hitting and longer-range, slightly lighter-armed variants. And/or try out self-guided missiles with active sensors versus remotely-guided missiles without. And/or trade off warhead strength versus hit chance versus surviveability for any given size.
I agree with Ulzgoroth's call for large time-on-target barrages - or, at least, the ability to "dial up" large barrages at will. At anything like equal tech, small barrages get shot down. That said, I dislike dealing with very large numbers of launchers on a single ship, as you can only manipulate them all or one at a time. I also dislike having to deal with very large numbers of ships; again, the interface makes them time-consuming to control.
All of these considerations combine to suggest standardized standardized multi-warhead missiles, with each sub-munition being relatively small. My designs of almost everything else vary greatly between games, but I have noticed myself gravitating towards size 12, two-stage, triple- or quadruple-warhead, ship-killers fired from either full-size, rapid-firing launchers or highly compressed launchers with long (>1000s) intervals between salvos. If you have or can open up enough range (you're not jumping through a defended gate, say), the latter offers advantages that include lower build cost and lower fleet training requirements.