The lower deck beams are an integral part of the hull strength, though full gun kits on the middle deck should be okay, having said that, the build will get quite messy if you intend to add full gun kits to the lower/middle decks, thats not to say it can't be done, but will need careful thought and planning.

The full gun kits on the lower/middle decks cannot be placed until the hull has been planked and gun ports cut/lined, so you'll need to hold off on the placement of the middle/upper gun decks for access to the lower/middle decks, and not forgetting that the lower gun deck had 32-pounders and the middle deck had 24-pounders, both of which had larger barrels/carriages than the 12-pounder kits, though you might be able to get away with the 12-pounder carriage as they won't be so visible through the ports and the barrels might look ok too.