I'm a member of the team that built the winning bot (the one that wrote most of the mutalisk code, actually). One of the things we found out is that, as an AI, it's completely possible to keep the mutas' dps up without clumping them -- humans mainly have to clump them because they can't issue individual orders every second. When the bot is up against corsairs or valkyries (or any other unit that does splash damage), the mutas deliberately spread out to avoid getting splashed. Corsairs are still a good counter, but our mutas can hold their own against corsairs much better than most players.
To address your bigger question, the choice of mutas was deliberate. Building any sort of unit controller is just hard and time consuming, so time constraints forced us to specialize, but we think we did a pretty good job. See another team member's post called "Overmind agent overview" for more details.