In fact some bootblock viruses can indeed damage a harddisk. Most of the older bb viruses are dirty written hooking the doio() vector of the exec.library. So if doio calls are made on a harddisk block 0 those viruses actually write themself onto block 0 and 1 (or more blocks) of the harddisk. If there is important information stored it is lost. Mr. Heiner Schneegold, author of the famous virus killer VT always mentioned in his doks that it is generally a good idea to have a backup of those blocks so in case it is possible to restore them.
Viruses like Lamer Exterminator are "better" programmed and check for trackdisk.device which is for floppy disks only.
But there is no known amiga bb virus which is able to spread itself or infect harddisks.