Don't worry, pause-resume is currently unreliable in general.
At one time it was for me, at least enough to pause the download if I needed to do something else with my limited bandwidth.
But not being able to finish a download at all is a major issue,
This issue will be fixed in the new version of downloader.
I see that sometimes the installer has a version number after it. Does this mean that sometimes I will get the "updated" items, but also be left with old, outdated files that should be deleted?
Yes. The downloader is only checking for the files it's trying to download, it won't check for any other files, no matter if they are called "setup_arcanum.exe", "folder.jpg", "widescreen mod.zip" or anything else. If the file isn't on the downloader's list, the downloader won't interact with it.
Correctly. Anyway, feature to perform hash check instead of name and size might be added in the next version.