Yes, I agree with Lazur that you can delete the unused patterns with File menu > Clean Up Document. However, be careful. If a pattern is not being used in the file (if it's not applied to an object in the file), it will be deleted by this process. So for all the patterns you want to keep, make sure they are being used, even if it's just a simple rectangle or circle.
As for giving them a name, it can't be done currently. But here's the feature request:
https://bugs.launchpad.net/inkscape/+bug/171952 To help push this up to developers attention, click "This bug affects...." which is in green text, near the top. Also gives it more weight if you subscribe to the bug (in the column on the right, click "You and not subscribed....." (also is in green text)). (However, subscribing to it means you'll get an email when someone makes a new comment.)
However, there might be another way to handle the patterns. It seems like I've heard about a way to add patterns to Inkscape. The patterns that you've created are only available in that one document. Unless you make the document into a template, they will only exist in that file. But it seems like I've heard about a way to add them to Inkscape, so they are available in any document.
Hhmm, after some investigation, it's not obvious how to do it. When you open patterns.svg, the file is blank. Looking in the XML Editor, the patterns still are not listed or enumerated. All it says is "Seamless texture provided by FreeSeamlessTextures.com". It seems to reference a JPEG image, in the XML, but I'm not sure how to display it. I think there should be a way to display it, but I don't know how. I'm thinking if I could display it, I'd try adding a test pattern to it. But after that, I'm not sure how to get the new file into the XML Editor. Seems like it should work in theory, but the logistics are elusive.
