Morale only matters for combat checks, ie, beam tohits (offensive and PD), missile salvos, and I think (but don't quote me on this) that low morale lengthens the time a fleet is acknowledging orders/takes to open coordinated fire if you have fleet training option turned on. Note, this to hit penalty also applies to civvie ships firing with cwis, so if you've got a troop transport or front-line tanker that relies on cwis turrets to thin the inevitable missile salvo that comes its way, don't use conscript crews if you can avoid it.
Personally, I think conscript is less conscript and more ships staffed by merchant marine types, which any decently sized empire is swimming in compared to the number of highly trained combat fleet personelle your academies turn out. I mean, it *is* a starship, even if you're going on the cheap you're not going to slap a couple hundred yahoos into it when you have potentially billions of compotent civvies to choose from. They're just not the ones that know how to properly react in a death or glory combat situation.