First of all, those models are really, really great.
I have always loved to add civilian stuff in all my wargames, to help for scenarios, just athmosphere, etc.
As for pinning, i think that every models has a gravity point where the most owners will drill a hole to add anything they want to base the stuff. So you could very well add a hole and it would help 99% of the people who bought them.
As for the exceptions, people wanting a special pinning, a hole in the lower side should absolutely not be a problem. At best, it's not visible. At worst, everybody today can add some green stuff to fill it.
So i would say drill a hole, a small one not to bother those who want to base the vessels with a particularily thin pin... And even, standard Epic holes where OK i think.