There are some differences between the free web edition (without a licenze) and the paid subcription edition (with licenze)
the main difference is, that the web edition won't produce all the files that can be used for production purposes and will allow you to test the functionality with some limitations (like time limited) this is some kind of evaluation testing ...
if you bought a licenze then you will also get some functionality, the web edition does not have (using more than 1 cpu core, and other enhancement) as well as additional ip functionality (FIR FFT ....)
next thing is, newer version will bring new features and enhancements.
a couple of quartus releases in the past, they introduced using more cpu cores than only onw to speed up the compilation time. or the MMU for nios, the current V9.1 will give the nios II e core free ...
but yes some changes also introduce that you must have an eye on you design if they will perform with the new version as they did with your latest. but they could fix bugs ...
any more questions ?