I can confirm this behaviour. I was using v3.8.2 (default on ubuntu 16.04) and then upgraded to 3.9.0 only to find that the multiple namecheap functionality has come and gone. Will be trying some intermediate version in the meantime. EDIT: I've opened a PR with a fix: https://github.com/ddclient/ddclient/pull/64
I'd like to clear up some confusion, the fix was actually committed a long time ago, but was recently removed again for some reason. This bug report has more details.
I can confirm this behaviour. I was using v3.8.2 (default on ubuntu 16.04) and then upgraded to 3.9.0 only to find that the multiple namecheap functionality has come and gone. Will be trying some intermediate version in the meantime.