They can present several issues:
1) filtration - hard to fit a sump or something under there so a cannister filter may be used which can cause their own issues. But due to the lack of surface area, gas exchange is limited, and therefor pH can be a problem. Circulation may be very critical.
2) Fish space, as mentioned, can be an issue. If you had for example a clown and an anemone, the clown may dominate the whole tank. This is true, of course, in smaller tanks but in hex tanks even decent size tanks still have a small footprint and are prone to territorial issues.
3) Lighting - not a problem with metal halide pendants but other options may be limited.