So, I just managed to scrounge together enough money to buy a bigger boat which has two slots for sails, armor and cannons. My question is do the slots for cannons represent decks or sides? Because I don't want to end up with a ship that has no cannons on one side or different cannons on each side (not good for my OCD).

The cannons will be added together, much like the rings in Sacred or Diablo when your character can equip more than one accessory. If you have a cannon that has long range with normal reload rate, and a cannon with low range but fast reload, then your ship's performance will be the sum of those. There are ships with 3 cannon slots.

Okay, thank you for explaining.

No problem.