Decks are just a duplicate layer of the slot layout; we have no direct control over what decks 2 and 3 look like.
The ship layout has 72 slots. The stock dreadnought layouts range from about 50 to about 70 slots total (with the Abbidon predictably fatter than all at 80 slots), so at least for stock, there should be plenty of slots available.
You can make the juggernaut use a base layout (88 slots, more than all stock races) if you need more slots. If you need even more, nothing stops you from using the slot modder to add another hull entry to the file with 20 more slots or so. If we ever get a neostandard se5 going, we can perhaps include a huge ship layout in the file.
Here is the base layout for reference:
http://www.spaceempires.net/files/temp/baseslots.gif