I do this to some extent, when playing with bases closely stacked. Usually I use trawlers to bring in nutrients so I can reach the 50% fusion engineer population that I crave!
However, they would tend to be within my 'perimeter,' established by deep-radar probe-foils and needlejets; that way nothing is likely to kill them off, armour or no. I have never used enemy territory. I find it's best not to put a temptation to attack into the AI's way, especially since it can't resist it.