To answer your questions in order...
Yes, the free floppy versions have a filesize limit of 4GB and the + versions don't. You can only fit so much code on a floppy
The free versions also have lower transfer rates (except the Gigabit ethernet versions)
Yes, the free version only boots from floppy. But NASLite is so stable you can leave the server on 24/7 without problems. I've had mine running continuously for months. Even if booting every day it would only add maybe 1 minute to the boot time to use a floppy.
I can recommend upgrading to one of the + versions, if only to get rid of the annoying beeping if your drives don't support SMART testing
Spend some time reading the different forums, I've learned a lot from them.