Can USB ports blow polyfuse on Raspberry Pi 3B?
Not if you mean when backfeeding power from the USB, because the ports are behind the polyfuse (ie., it provides no protection that way). However, that means it does protect against shorts in USB devices (when not backfeeding), although I think the USB current is limited such that maybe a surge of that sort would not happen.
You are not really talking about that either, although the "maybe" there would be the only situation in which a problem with a USB device would trip the fuse. But I don't think the fuse is your problem. The fuse doesn't just kill somethings ("after every day or so all the USB ports have no power"), it cuts power period until the fuse resets.
I have heard that some powered hubs (and so possibly also drives and other devices with their own supply) do potentially backfeed power. This shouldn't be an issue if there is a proper common ground and the voltage is regulated properly, but a misbehaving/broken/defective device might cause problems.
Note that there is no separate polyfuse just for the USB, but someone else has reported your symptoms here:
Raspberry Pi 3 Model B (not B+) USB polyfuse location
Unfortunately the conclusion seems to be that it is because of irreversible damage