Fleet speed: When I field such flak barges, I typically have separate fast and slow fleets. Slow ones are built to deal with any expected missile threat, deliver one solid punch outside beam range, maybe a little cleanup capability (e.g. nebula-conscious designs with microwaves or large low-tech lasers). Fast ones are designed around dominating the opposition by being both faster and longer-ranged, with modest self-defence capability in case I need to deploy them into a messy situation.
Trade-offs regarding availability become tricky especially once we view the whole lifetime. An obsolescent battlecruiser, once the pride of your navy, may languish in a hangar because it's not worth the upkeep costs... but when the need arises, it can support a modern fleet without slowing it down or run down enemy assets where you don't want to risk your current ships. Ships that were bottom of the barrel even when new may be cheap enough to operate indefinitely, for PPV and as a first line of defence.
Small missiles: These mostly suffer from poor fuel efficiency. This is not normally a problem for quite some time, because I'm stingy with power multiplier and agility tech (the latter means I'll use relatively large engines for the missile size). It may be different if you're willing to splurge on techs that will mostly affect your missiles.
I definitely prefer volume over armoured missiles, however splitting them up into single-missile salvos is often the most effective way to overcome point defence. Preferences may depend greatly on details: I generally like size 7 or above box launchers, size 1 full-size launchers, and reduced-size launchers for those in between.
