I think it depends on the agency. If I were you, I would first feel them out and get a feel for they link build with their clients. Maybe take a neutral stance on everything until you can get deep enough in the conversation to figure out how aggressive they are with their clients.
I know of agencies that do both, so your best bet is to first find out what they do. One tactic you might want to do is see if you can go on their website and view the portfolio of their clients. If they list some of their clients, you can do a backlink check on the clients website and examine their link portfolio. If they have a bunch of spammy links, etc. then you could probably make the educated guess that they would be more open to automated tools. Hope that helps!