I thought I read in a thread post *somewhere* that the shortcut kets etc... will work in the commercial version. No need to worry.
My hope is that there will still be a browser-based version synced with your offline application or even with your Steam-version (if any). It's good if you have some quick spare time left and you can't install something on your PC. (e.g. if you're taking a break at your work but don't want to contact the admin three office ranks above you asking to install Desktop Dungeons.)
I also hope it comes in a ZIP/RAR/7z file like the freeware does. So it doesn't mess up with your registry, and you can just copy the entire folder to a USB-stick and take it elsewhere, or play it directly from your USB-stick.
Lastly, what will you do against piracy? Is the client free downloadable and you have to login, like in World of Warcraft and Minecraft (so you're paying for your account, not the application itself) or is it just the regular client that's paid for?