I don't like folders anymore. Whenever it's possible I store the objects directly in the product. There is also a preference to disable the folder view on the left site.
The question is, do you work in one huge product or split it in to different modules library? Isn't that PTC's concept behind Product / Library?
Most customers I know are using few huge products and store anything in folders, but at the end they start "arguing" in which folder the part and documents are stored. Or even worse, they start storing it on the lowest level, because they don't know where to move them.
Another popular concept is to create folders for parts, cad, documents, change objects, etc. These are actually filters and nothing else.
There is no right or wrong. In early days I also had a huge folder structure in my mail account, but since gmails entered the market, I have no folders anymore and I search and don't navigate anymore. For me, the work is in vain to move the mails. I prefer to search.
That is also the reason, why I'm looking forward that Windchill improves finally the search. Solr isn't bad, but it could be much better! I would prefer a google like search to find everything and start filter afterwards. At the moment, the search is not yet very user-friendly and intuitive.
To come back to your question. I think setting the table size to 1000 or default 2000 is more than enough.