I think we're talking about two different things here. 1 is the list on the front page of limewire of all the files you are currently downloading. The other is the list in the incompletes folder.

I usually "clear inactive results" in the front page download section regularly (this takes out the "awaiting sources"), and it is much faster than selecting the files in batch. You must really be downloading hundreds of files simultaneously. This definately slows limewire down.

If I can't find results after a few hours of being connected, then I abandon hope of finding them (at least that session). I have no need to keep tons of files in the download section.

I do occasionally resume incomplete downloads to see if they are available at that time. But instead of clearing the 0kb files from the incompletes folder in limewire it sometimes is faster to just delete them from the incompletes folder. If your files are not in the downloads section they won't show up again in the incompletes folder.