So it doesn't matter if I install pirated stuff on sys cfw it'll effect both stock & sys cfw?
That's how I understood it back when I was researching what I can and can not do on a modded Switch if I want to be able to play online as well. Both sys CFW and stock system share the same NAND. With the emuNAND, things are a bit different. You're making a clone of your sysNAND and by installing pirated games you're making your emuNAND "dirty". If you block the Nintendo servers, blank the prodinfo and stuff, you're less likely to get your console banned.
don't have the original backup but I guess I'll keep it offline unless there's a method to clean it all
Sadly, the only safe way is to restore the clean NAND backup only if you haven't connected to the Nintendo servers after you created the backup. There are tools that clean your logs but that will trip the log mismatch and flag your console.
other than that how do I update the sys cfw
I'm not entirely familiar with the sysNAND CFW, but I assume that you can update it via the official way or via Daybreak. It should be the same, I think. Better wait for someone else to reply, someone who's using sysNAND CFW daily.
& I have installed few games but some of em are not loading what's the issue with it?
There are many things that could stop games from working. What did you use to install them with, which installer? Tinfoil, Goldleaf, DBI, etc.? Did you boot into CFW without up-to-date sys-patch/sigpatches? Game tickets could've gotten invalidated depending on the way you've installed those games. I usually suggest reinstalling the games with the latest DBI while having the latest sys-patch, that usually fix the issues. Make sure that you have the latest patch as well. Not 100% necessary, but sometimes games will start working again if they are up-to-date.