I can think of a couple issues with using a onion address instead of clearnet.
- Not all forum and wiki visitors use Whonix/Tor. ( Think first time visitor- Whonix curious? )
- A Whonix user may visit the wiki/forum to troubleshoot for an inoperable system. They may have to use a clearnet browser.
I think when it comes to Best Practices onion would be the choice. Another thought, would it be plausible to have both clearnet and onion when available? I know it would be a pain in the …