Survey ships are now armed at the start and their point is like all pirates/barbarians in similar games is to hamper and harass you in the early stages.
Usually they serve to make you have a military early on and to be easy XP farms for your units. Of course the latter doesn't matter since there is no ship XP (though Paul suggested that with fleet admirals get put in XP would return in conjunction with the admirals rather than the ships). Plus early threat is a good thing.
The pirates are also not fully implemented so the anomaly guys are just part of a greater whole.
