Your search won't work. You can however make the tables a bit smaller by adding common stopwords to your language packs stopwords file. Try running the query:
SELECT sw.word, COUNT(sm.post_id) AS hits FROM search_words AS sw INNER JOIN search_matches AS sm ON sw.id = sm.word_id GROUP BY sw.id ORDER BY hits DESC LIMIT 50
What you'll get is a list of the 50 most common words in the search_matches table. If you find any words in that list that you consider to be stopwords (i.e. words that we use to communicate but doesn't really "mean" anything), you can add them to your stopwords list and rebuild the search index in admin/maintenance.
Edit. If you feel like it, please post your results here. I might have missed a few common stopwords myself. I've added the following stopwords in 1.2: now, well, ive, really, thats, ill. Please note that all words are lowercased and singlequotes and such stuff is removed before the words are indexed, so "I've" should be "ive".
"Programming is like sex: one mistake and you have to support it for the rest of your life."