I think i had something similar a couple of years ago
with DHTML menus. Even at 10 drop links it went sllllooooowww.
Maxed with 5 and everything corrected its self and speeded up.
Can you not just make a single table full of all these
1,000 links on its own dedicated page?
Or throw them in a db ??
And then link to the 1,000 link page as "links"?
Simple sometimes is your friend