Q: are the private keys stored in nodes hard drives/wallet files?
A: Your Private keys only stored in your wallet.dat file.
Q: can someone use any data from blockchain or nodes wallet files somehow to use the data in key collision attempts?
A: No, no one can use or sign any data in network, because network accepts those data which only verified by miners and miners only verified real transactions which is assign using a valid Private key.
Q: last one, what happens if I remove the ticks for all kinds of files and folders in the index configuration of my windows machine and run Core wallet as well? does that in any way effects the performance of my Core wallet as to creating any issues for proper syncing?
A: no its not effect your wallet Syncing.
