It's very unlikely that the tables added by plugins would cause slowdown, because if the plugins are not there the tables won't be used at all.
If you have many options in your qa_options table (over 1000) then it could be causing slowdown. There are around 300 core options so more than that means they probably came from a plugin.
However, it's difficult to find exactly which options are not being used. You'd have to look at all the plugin code to see what options they all use. You can look through the qa_options table (e.g. using phpMyAdmin) and if you see options named for a plugin you removed, you can delete those options. For example in my Tagging Tools plugin, all the options start with "tagging_tools_".
