Can I use APT over Tor?

Yes, deb.torproject.org is also served through via an Onion Service: http://sdscoq7snqtznauu.onion/

To use Apt over Tor, the apt transport needs to be installed:

   # apt install apt-transport-tor

Then replace the address in the lines added before with, for example:

   # For the stable version.
   deb tor://sdscoq7snqtznauu.onion/torproject.org <DISTRIBUTION> main

   # For the unstable version.
   deb tor://sdscoq7snqtznauu.onion/torproject.org tor-nightly-master-<DISTRIBUTION> main

Replace <DISTRIBUTION> with your Operating System codename. Run lsb_release -c or cat /etc/debian_version to discover.

Now refresh your sources and try if it's still possible to install tor:

   # apt update
   # apt install tor