The puppets will work merchant slots and produce MoV's, it is not possible for the capitol to work enough science slots to prevent this. You can slow it down though. If you send a food route back to the puppet, the puppet will also work science slots and will produce GS's as well as MoV's. This is all a moot argument anyway. Venice is geared to diplo victory. Diplo has the shortest tech path, you do not need a bunch of GS's for it. The extra MoV's produced by the puppets have no effect at all on turns to victory. You will always get a minimum of 4 GS's, you need a total of 6, the last 2 can be faith bought, or taken from Pisa and the PT.