Great questions. I will speak to the kayak question. We carry three kayaks on the roof and three bikes in the bed of our Tundra. We use the Hullavators for the two outside kayaks closest to the driver and passenger doors. They are $600 or so a piece but they make it so easy! There is varying info online as to how much weight your truck roof and the Hullavators can accommodate so you would have to figure out what you're comfortable with.
The main advantages of having the kayaks on the truck roof:
1: Not having to walk around them in the trailer every time you go in which will be far more often than you think (lunch, bathroom break, forgetting something inside the trailer, etc).
2: Once at a camping area you can depart to any body of water in your truck with kayaks on top without having to move them from trailer to truck.
The only disadvantages I can think of to carrying kayaks on top of the truck are some bug splatters, decreased truck mileage due to wind resistance, and perhaps theft though this can be mitigated with locks if that concerns you.
Of course, cleaning/drying off kayaks each time before putting them into your beautiful trailer would seem bothersome to me but I've never done it so it's just speculation on my part.
You're smart to be thinking all of these questions through as best you can because come "camping" time the easier it is to get to the toys the more pleasurable it is and the more you want to go!