If there aren't reasons, security or otherwise, for blocking certain file types....I also wouldn't mind seeing .install, .inc, .php, .patch, .css, and .js added to the list.
Well, yes there are security reasons. These are blocked by .htaccess because you don't want to allow people to download the raw source code for your site implementation! (.module, .php, .js etc.). I guess it's possible to allow these file types only for certain subdirectories (although I'd suggest thinking very hard about code injection attacks before doing this), but is it really a problem to just zip them up before you post? Saves space/bandwidth at ubercart.org that way too.