.htc files are used for IE6-9 compatibility, so I don't think there's a practical downside nowadays .
.plist files are just used for the .hype document restoration feature and are not used in the rendering of the page at all.
The 50 file limit is probably the bigger concern as a lot of projects get past that (especially considering retina and non-retina versions of images might be generated, doubling assets). But if it is a small document then that is not an issue!