If I encrypt my wallet but before doing so save the unencrypted .dat to a usb stick, will that .dat still remain password free even after I encrypt the wallet on my PC or will it also become encrypted?
Encrypting is an active process.
If you don't encrypt your wallet.dat, it will stay
password free until you decide to do so.
2. Is there a way for a hacker to steal my .dat via virus and if so how common/easy is it to do?
If you are targeted directly in an attack, it probably wouln't be too hard to compromise your system (assuming you don't have any further security precautions).
Even in a properly updated system maintained carefully there is a medium risk of getting compromised by 'every-day usage' of an computer.
Even if one is not targeted directly there is quite a big risk (through *.dat stealing malware) to lose confidential wallet files.
You should not store big (relative to your holdings / what you can stand losing) amounts on a desktop wallet.
For amounts you really don't want to lose use either a hardware wallet or a paper wallet to store them offline.
my wallet says that my coins are still there but it's not synced now so I'm not sure how accurate it is..
You can always check your balance through a blockchain explorer if you don't want to wait for finished sync.
E.g.
https://www.blocktrail.com/BTC or
https://live.blockcypher.com/btc/I also did a deep scan and my computer found 4 suspicious files. So you could say I'm shitting myself.
You should remove all suspicious files and check whether everything else seems fishy.
Do further checks of your system and remove anything suspicious.
Make sure to backup all important wallet files. If you want to be sure your system is clean you probably should use a fresh OS install.