You're right, of course...managing SSL certificates with websites could certainly be made a lot more user friendly with not having to drop down to the command line being the ultimate goal.
To answer your question on why...it's all a matter of resources and priorities. There's three ways for things to get developed in ClearOS...
1. ClearCenter to invest resources to have paid developers work on the feature
2. Volunteers from the community to commit time to a project
3. 3rd party developers to create apps/extensions that are installed via the Marketplace, with the option to charge for the app to recoup time invested
For what you're describing, only 1 or 2 are really viable since (#3) it's difficult to take a free app, make it better, then charge for the entire app for the new feature.
So now you're down to whether ClearCenter can see an ROI and whether this precedes all other development going on or someone finding time in the community.
At ClearCenter, we've discussed better integration since many don't know that we resell signed certs from providers Thawte, Comodo and GeoTrust, so there is a path to an ROI...just nothing that outweighs some of the other stuff going on.
I've added it to the bug tracker as a feature so it can be commented on and viewed by others...but that's about as far as I can guarantee it goes for the short term.