Yes but not by default.
C-lightning uses a pluggable Bitcoin backend. The default one, bcli, will use the bitcoin-cli executable to make requests to a bitcoind.
It exposes bitcoin-cli's rpcconnect startup option to lightningd which does not not support onion hosts. And you probably don't want it to as it is not meant to be exposed.
If you want to run C-...
I found the answer. It was not too hard. You should make a separate Tor hidden service for the ElectrumX server. The following two links helped me:
To create a hidden service, you should take the following ...