Any reader that indexes the metadata of books to group them into collections, shelves or whatever, will slow down considerably when you load 1000s of books on them. That applies to Kobo, Sony and Kindle. That is simply because indexing takes time.
If you also want good performance you might want to consider one of the brands that use a simple folder structure, e.g. PocketBook or Onyx. A bit more difficult to buy where you live, but not impossible. Integration with Calibre is very good in those situations; you can let Calibre build the folder structure for you.
As to the pros and cons of tags vs. folders, we've discussed those elsewhere in these forums. A little searching might help you. In the end, it's a matter of personal preference, but I thought I should at least mention this performance issue to you.
I'm also the kind of person who carries his entire library around, and that is one of the main reasons why I did not go for the 'major' brands.
Last edited by Zetmolm; 10-06-2012 at 04:19 AM.