Update - not seeing a neogeo.ini
There isn't until you make one. It replaces mame.ini settings though, which IIRC do not include key mappings.
See my post about the ctrlr folder above.
Back when I set up HLSL on v.146, I made a neogeo.ini with the HLSL settings I wanted to use on all the Neo Geo games.
You can also make vertical.ini and horizontal.ini files to have different settings for those particular games.
.....at least you could back when I set everything up. Things may have changed by now.