If you decide to go the root or custom ROM route, you'll have no issues with that because you can determine whether you want them to get called up or if you want them to appear permanently. On the stock ROM, as mentioned above, they only disappear when you're watching a video or doing something that requires the full-screen, which in my opinion is pretty smart - I don't get why the extra second of pulling the buttons up would be that much of a hassle for someone?
I am coming from the M7 as well and I was actually pretty paranoid about not having hardware keys, but I can tell you that the on-screen buttons are miles better and more convenient than the hardware ones (and also much more responsive, of course).