lucy24 - 12:03 am on Feb 2, 2012 (gmt 0)
5-6 SECONDS?! How long are your query strings? Or rather, how deep are the queries nested? The top layer should always come through as a literal ? while the others get converted. The question has come up more recently than 2010; I remember pawing through raw logs to find something with nested queries. (In my case, it was piwik passing along search-engine information.)
Normally a query means you're going to a php or similar page that deals with it. Feed the whole thing into the disencode function (don't remember its formal name but you know what I mean) before anything else.
You shouldn't have to involve htaccess at all unless you're converting incoming queries to pretty URLs. Is that what you're doing? If so, we need to figure out what order to do things in. 6-7 seconds is definitely over the top unless you have the world's slowest server.