I'm pretty sure that DexNav increased chances to ~1/200, I can vouch for that considering how many shinies I've found in ORAS randomly through DexNav while looking for specific egg moves, HA, IVs etc. I found like four shinies without a conscious effort within like two hours recently on DexNav.
So yeah, I miss DexNav a hell of a lot. I'll undoubtedly still use it a lot to catch Pokemon to transfer to SM because it was so efficient in getting good Pokemon in the wild. I know they recycle and remove features a lot, but I was still super hopeful that they would retain DexNav in some way. I guess SOS battling is their way of doing it, as annoying as it is though.