having been in the sport years ago as a crew chief, i can tell you that both have advantages and disadvantages.
manual
pro's;
lighter, variable launch rpm
con's
inconsistant even with the best drivers, and missed shifts(even by the best drivers).
auto's
pro's
consistancy of launch rpm, shifting, and virtually NO missed shifts.
con's
weight, complexity.
in the hands of a top driver either does very well. for the average driver the auto is going to be the better choice overall.
by the way, 1320 top fuel cars have NO transmission. their "gear changes" are accomplished by locking up the clutch in stages. this actually occurred in the late 80's when kenny bernsteins crew chief came up with the idea of locking up the clutch at the 1000ft mark(yes back then they had a two speed trans) or so, giving what was essentially a third speed. teams then started experimenting with eliminating the transmission completely and locking the clutch up in stages, first with electronics, then with pnuematic timers when the nhra outlawed the electronic controls.
by the way top alcohol cars still run three speed transmissions.
prostock cars use a lenco trans where the clutch is used only when launching the car. nextel cup, and many other stock car classes use a clutch also to launch the car, and dog rings to allow clutchless shifting, up or down.
there was also, at the time i was racing, a popular modification whereby you put a clutch in front of an automatic trans to eliminate the torque converter, but still keep the consistant shifting qualities of a manual valve body automatic. the two most popular ones were the clutch turbo and the clutch flite transmission, often dubbed the poor man's lenco.