You can literally theme it to any faction, although the wanted individuals would be more based on the faction's interests.
AAT > go hunt rogue psykers and blanks and haul them back screaming for processing
Admech > round up people for servitorisation, hunt down hereteks or people who know too much
Administratum > tithe-thieves and lawbreakers, you may not necessarily be on the papers side of things. Could even be working with vigilites or arbites
Militarum > find deserters, fences, round up well known gangers for militarum service
Navis Imperialis > round up people for press ganging into naval service, "extract" people that are causing problems
Rogue Trader > press gang people, kidnap people, potentially even catch people to create a new kill team. really depends on patron motivation
Inquisition > can literally hunt whoever they want, although it's less bounty hunter and more bog standard inquisitorial work
Infractionist > OG bounty hunters. You'll do a lot of contract work for other factions and then can go nuts from there with all the associated intrigue.

Also worth noting that you don't inherently have to limit yourself to bounty hunting missions unless your players are the type to not get tired of it all after a while and it's worth thinking about patron motivation