There is a question about the prowlers: where to get them? I've only come across a few during quests, and those that bounty sometimes turns into are immediately killed when you knock their HP down to zero, even with non-lethal weapons.
As far as the bounties go, I have never been able to capture a target from one of the daily bounty mission from City Hall alive. I explain that by these being 'kill orders', not 'dead or alive' and the game is simply making that happen for the player. Some of the specific bounties *can* be taken alive, like Tuner, so I don't know if it's intentional or left over from before males were capturable.
I don't know of any renewable source of capturable prowlers.
I was able to capture the undead priest inside of the temple of doom area. Otherwise yeah the main target of a daily bounty doesn't seem to be capturable and those abominations never have friends.
Having an abomination in your household for long is not great though. They can't do anything and they lower the happiness of anyone in your household with less than 40 willpower by 2 per day
You can get prowlers by capturing the space marines during the quest "Taking Down the Hulk". The Hulk himself is a generic prowler too.
The total you can get from there is 5, I never tried to capture any in the The Prowler in the Depths storyline, but since alexsis987 said they caught the one in Temple of doom I would assume those are capturable as well (I haven't tried that either). I also believe there was another quest (one of the slave's stories) where you went to a research facility and there was an option to kill a prowler or add it to the household.
From the looks of them the only use for them is either donating to Fort Sera or selling them to Hunt Research, iirc the price was 7,500 $ per prowler.