This is how science works. you look for gaps between theory and observation, you postulate new theories or upgrade new theories that fill those gaps. You then use these new/improved theories to make predictions about unknown effects that can be measured and experimentalists look for these effects and if they find them you might win a noble prize (: dark energy/matter probably do exist and the scientists should find out what they are within the decade, but if they don't find them then thats more interesting as it would indicate that theres a really big gap in our understanding on the universe.
What you say about dark matter is also true for quantum mechanics because despite its huge success in explaining how the small works, its still an abstract mathematical struct. There's a nice artical about people are are looking into the reality that is behind QM is new scientist, available here are a few weeks before its paywalled Is quantum theory weird enough for the real world?