Fair enough, it is an expensive keyboard, so any major issues you have with it make the price harder worth it.
I don't use tilde much.
There is no absence of a super key. Its on the spot where alt often is, and alt is on the spot super often is. It shares key with shift.
The ctrl is where caps lock is on today's keyboards. If I have caps lock I rebind it anyway. So ctrl and super are easiest to reach, whereas the spot where ctrl often is is difficult to reach (there is nothing there on the HHKB).
So in short this keyboard assumes you normally rebind caps lock to ctrl, it assumes you never use the ctrl elsewhere. It assumes you use super more than alt. It is pretty close to a traditional Sun keyboard.
Funny thing is also, you can buy the keyboard without print on the keys, so that you can rebind it in any way you prefer.
What?? I use it all the time: Tilde in vim for upper/downcase and bash for home and backtick for jumping to marks and in JS for template strings. Great key.