Yes, transport encryption (you can call it "end-to-end encryption between server and clients") is used everywhere by default in BBB. TLS is used for any TCP HTTP traffic, and dTLS is used for the UDP RTP traffic. The WebRTC connections are thus secured using DTLS-SRTP, and fingerprint checking is implemented - the fingerprint for the dTLS certificate is transferred over the TLS secured websocket connection (DTLS-SRTP) to the client. The defaults configuration of nginx HTTPS webserver site (part of the BigBlueButton server) contains a pretty good and tight configuration and is very easy to adjust / tighten further if needed. TLS client authentication can optionally be configured/enabled there, if needed.
If you have any more questions about any details, please feel free to ask!