McGoo

This can happen with any CMS as the themes are built around the current hooks implemented by the developers. You're unlikely to find a CMS that this doesn't happen with.
 
 
Again, this is usual with most CMS that if you keep it up to date it will remain pretty secure. All the current CMS creators out there have documents on their sites about how best to be extra careful with security, so it's best to read these and follow them carefully
 
 
By it's very nature, a CMS should be easy to use as it's a consumer facing product. Any CMS that is hard to use is counter-intuitive of it's reason for being built in the first place. A CMS is primarily for the not so developer friendly to be able to update and maintain content on a website. Any CMS that makes this difficult has already failed in its main task.
 
My personal favorite is WordPress. It has a good combination of being easy to use, secure and generally updates don;t cause to much of an issue to themes as they tend to work a lot of backwards compatibility in on each release (much to my annoyance).
WordPress has recently released version 3.5 that included major work to the whole media management area and i've yet to see it break any of my themes and it was quite a major update. There's always time though