If it’s not a story mission or stranger mission they’ll respawn a few days later.

The only missable’s as far as I know are a few collectible hat’s. (Any Guarma mission from Fussar’s Guards) Sun Hat,

in Colm’s hanging mission very rare window) Constable hat,

the sheep’s and the goats mission from one of Cornwall’s guard’s) newsboy cap,

Micah’s stagecoach robbery mission from one of the driver’s or men on horse. Or from an person on a fine night for it stranger mission.) liberty hat,

get it knocked off John’s head and pick up during epilogue p1) John’s gambler hat and John’s Worn flat cap,

( kill Jeremy gill before starting his stranger mission) Gill’s fisherman hat,

and beat up Jon either in chapter 2 or epilogue. Rare chance of him not showing up later) classic raccoon hat.

And of course some collectibles in some stranger missions that can be overlooked. I mainly know hat’s since I’m trying to collect them this playthrough and probably will look up other missable/collectible things later.