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.
I eventually got round this issue by taking a long shot and searching in the Registry using RegEdit for the phrase "Multi-Device" in any reg key associated with Visual Studio 12. I found in:
HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\12.0\JavaScriptLanguageService
An entry called ReferenceGroups_MDD.
What I actually did was remove the whole thing from JavascriptLanguageService down but I reckon you could just remove that one single key. Voila! Update 5 installed.
I hope this is of some use to others who also get stuck with this.