I thought I should post this here to help anybody else encountering this problem when installing the new Update 5 for VS2013.
I spent about 3 days now trying to install Update 5 for Visual Studio 2013 with the installer saying the update is blocked due to there being a version of Multi-Device Development for Hybrid Apps (MDD) already present on the machine.
I had removed the CTP of MDD but obviously something was still lurking on the machine that made the installer think that it was still there. I checked out a bunch of threads like this one relating to the problem in earlier Updates of VS2013 and also this article on Microsoft Support. I found no trace of the referenced files in Package Cache.
Below is the fix I found.