In terms of performance? Not sure. I would suggest that you ensure
that scanning takes place when nothing else (like crawling a content
source) is occurring.

If you mean the virus  scanner scanning the index, I would strongly
suggest that they not scan the indexes since there is always the
possibility that some portion of the index  will innocently look like a
virus and the scanner will attempt to fix it.

hat location are the sharepoint  index files in so that I may exclude
these from server  side scanning?

By default, under the c:\program files\sharepoint portal server\data directory.

And if it's Windows Sharepoint Services ?

Then it is under the bin directory in the 60 hive.