Yeah, I've never done any over about 5,000 notes - I think once you get much above that, the graph would be too crowded to get much benefit out of, anyway. (The sweet spot for a pretty graph where you can actually see multiple patterns is about 100-500 reblogs, I think, which translates to around 1000 notes.) (I'm not sure there's actually any "data collection" involved in this though - Fusion Tables network graphs are really more about pretty visualizations than actual useful analysis, so far, and if you want any more sophisticated information from the data you need a more powerful spreadsheet program.)

I don't know if there are any extensions that will let you see all the notes on a page at once; that might help. Although at some point you're probably going to crash Fusion Tables with too many nodes and have to move up to Gephi anyway.