For one there's been a push to have hardtop convertibles which I think are awesome. Second, I don't know much about modern safety standards but I'm sure it's more difficult to get a 5-star crash rating with glass overhead. Also, as mentioned before they can be a bit of pain when it comes to removal. For a day of driving they're great, but if you're just tooling around town on a sunny day, the convertible and the sunroof have them beat.
"The 300ZX Turbo is a dance; it's a song; it's rolling, roaring automotive art. There is no color that doesn't suit it. There is no mood-lifting chemical substance it can't replace." - Automobile Magazine