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 …
These used to be on download.whonix.org, which is a different subdomain. Hence, no relative links were possible. Therefore there were two downlaod buttons, Clearnet + Onion.
This was non-ideal for users using the onion. If they pressed the main (clearnet) download button, they would have been redirected to download.whonix.org, unless they pressed the onion symbol.
This was greatly improved. download.whonix.org is now also available from whonix.org/download. Therefore relative links can be used. This means with only 1 download button, all will be as expected. Visitors on the clearnet website will download over clearnet and visitors of the onion will download over onion.