I am on 9.0 sysnand version. I currently only use theme hax to access my 9.9emunand. Can i update my emunand to 10.3 and still use them hax as an entry point?
Sure, updating your emuNAND has no bearing on your sysNAND at all, unless you accidentally update that instead. There's no reason to keep your emuNAND on o3ds on anything less than the current version, unless you use Gateway (sometimes the multi-rom menu won't work after a new firmware update).
It is, but at the moment, there isn't a single game that 9.5 emuNAND can't play (and eShop is still accessible via HANS, or installing the latest eShop CIA via Gateway, along with NVer), so being stuck there is no disadvantage.