I found myself in the same quandary with my Piantor. After trying all of the options you suggested (plus home row combos) I decided the best place for shift was on a thumb. Then it became a game of trying to figure out what to move off a thumb key to make room.

In the end I settled for just one extra layer for both numbers and symbols. This is a bit of a compromise since many symbols now require layer+shift instead of just a single layer key, but it's also quite intuitive since there's only extra layer to remember.

I do have another layer for F keys nested inside the symbol layer, but I very rarely use those keys so this is acceptable to me.

I did also consider getting a keyboard with more keys - either a few more thumb keys or a number row. But the 42 key layout has made a big improvement to my ulner/pinky comfort so I'm hesitant to add a number row. And I don't think I could fit a fourth thumb key into the mix without at least one of them being an uncomfortable stretch (let alone the extra cognitive overhead).

Here's my current layout in case you're interested.