According to this Reddit thread, if you rebind your keys so the primary keys are the Numpad numbers and the secondary keys are the regular numbers, then change the primary keys back to regular numbers, then change the secondary keys to the numpad numbers, all the options will show only numbers. I tried it and it worked like a charm. It's not removing the numbers altogether, but it's not as obnoxious.
It feels to me that there is a bug occurring.
I played around in the key bindings and it seems some options are showing the primary key, like the upper and center-right options, and the other options are showing the secondary key. One would think they should all show the primary key binding.
By default after the April 6, 2017 patch, all dialogue key bindings have the regular numbers as primary keys and numpad numbers as secondary keys (my keyboard has a French layout):
However, changing the secondary key to the primary one or removing secondary keys altogether changed nothing in the dialogue wheel. After removing and changing the primary and secondary keys many times, the best that happened was the upper-left choice changing to a regular 7. Every time I changed that key, I had changed the keys for all other options, yet those stayed the same.