From what I recall, some things will be taxing, like the quick navigation feature (that might be removed in XF2, actually, since I don't see it anywhere).
But 1000 forums is very excessive. Even the prefix capabilities would not be the ideal solution for this. Tagging is probably your best bet, with some custom add-ons to emphasise the tagging more, or tag based categories even, but 1000 forums would indicate a design problem tbh.
Also, there's only 1000 companies in India?