Do Virus Scanners Scan Hidden Files

hello not been on for a while but have a question while backing up a customers files
viruses/add-ware and root kit found
tried the usual programs we use ie combofix/malware bytes and cc-cleaner as well as eset nod 32
reg cleaner and the like but as the computer is full of junk programs decided to backup and format on which i found hundreds of hidden files

but this has got me thinking do programs like antivirus/add-ware and the like scan hidden files or do you have to un hide them first