HHKB doesn't have a layer 1 caps lock, its on the Fn layer on Tab IIRC. I don't remember the last time I used capslock, and I use TMK on my HHKB anyways now. Pretty sure I don't have it bound anywhere.
My Pok3r, nor my Varmilo TKL have a capslock key either. On my Pok3r its Function, and I've remapped it to Control on my Varmilo. Key chords are easier with Control in its proper location next to A.
Its probably more ergonomic as well. You have to move your hand to use Control in the corner. While you can maintain the same position when its next to A. Or at least, there's less movement.
If you do key chords often, it won't take long to adjust. The only chord that gave me problems was two handed ctrl+alt+delete, but that's probably because I tended to do that after I was already standing up. I fixed that by switching to Windows+L instead. On a TKL or full-sized, when sitting at the keyboard, I have always used ctrl+alt+delete one handed.
So, quirky stuff like that aside, it was a pretty easy transition. Control+letter chords became second nature within a few days.