Technical POV , if any security software can't SCAN Hidden Files, i personally won't even Label it as a security software.

That being said , Avira can Scan Hidden Files.

Simple test?

1) Create Folder A
2) Create Subfolder B inside Folder A and make it as Hidden
3) Demand Avira to Scan Folder A
4) Check out the Scan Reports and see if it scanned the subfolder B

Answer? Yes its scanned. End of story