Re: Agents of SHIELD season 2 News, Rumors, Pics, etc. until release..
SHILED in the comics have a lot of LMDs that aren't actually used as decoys for specific people. Just that I can remember, I've seen random ones running secret hideouts (before AoS Koenig and after). Tere was also one I swear was said to be used for spy work (it was mentioned as a "seduction" model or something like that, although I don't remember the specific comic it was mentioned in).
They seem to be used like you'd use a robot, in places they don't want to use human agents, although they apparently don't trust them/don't have enough/the expense is too great to make LMDs the majority of SHIELD agents. LMDs have been known to go rogue too, so at least some are sentient, although I'd assume that's not common. Honestly, seeing a LMD actually used as a decoy, unless they're a Nick Fury LMD, is probably the least common use for them I've seen in comics.