bitcoind – Scan ports for my onion bitcoin node and RPC calls

1: How can it be scanned? how can I see if its exposing any port, or port 8333?

Use getnetworkinfo RPC and results should have one onion address and port number mentioned if onion service is created for Bitcoin Core:

localaddresses": [
  {
    "address": "omy7kj7zwvfg5luayideh73uqb2latkoyyy5h65y4atv3fymnlxlzwqd.onion",
    "port": 8333,
    "score": 4
  }
]

2: How can I make RPC calls through Tor?…. maybe this is not the best way because of security for the RPC API and calls in plain data.

Check instructions mentioned for proxy,onlynet=onion and it’s trade-offs here:
https://github.com/prayank23/bitcoin/blob/tor-docs-add/doc/tor.md#1-run-bitcoin-core-behind-a-tor-proxy