What is the difference betwenn a 12v 7ah battery and a 12v 9ah battery apart from the amps/weight/size.
Just the price probably. The 9Ah has about 25% more capacity than the 7 and will be a bit larger and heavier ... and more expensive of course. That will give you a longer run time, but it might be too big and/or heavy for your boat. If weight, space and price aren't a problem generally go for the larger Ah to get longer runs - if you think you'll be on the pond for long periods.
Also can I run a set of LED navigation lights from a 12v SLA instead of using a small 9v battery?
Yes, but if they are built for 9V you'll need a voltage reducing system of some type to drop the excess 3V. If you are building/assembling them yourself you should be able to adjust the resistor values for 12V instead of 9 without any extra work.
Oh, I see this is your first post, so welcome to the
madhouse Mayhem.