To remove the () you can open the app\design\frontend\<YOUR_PACKAGE>\<YOUR_THEME>\template\catalog\layer\filter.phtml and comment out the
(<?php echo $_item->getCount() ?>)
However, to fix the issue it is better to open the Admin > System > Index Management and update the indexes. Then open Admin > System > Cache Management and flush the cache.
Btw, if you need to modify the “Shop By” section of you site to make the shopping experience much more pleasing, you can also consider Improved Navigation addon.