There should not be a significant difference in price. Other racing transmission vendors offer both configurations. The advantage of a sequential shifter is that it is idiot proof at least in racing dogbox terms. You can't misshift (I'm sure some will try) because you can only go up 1 gear or down 1 gear. It is one less thing to distract you and as as result you will make fewer mistakes. It doesn't take much to lose a position shifting from 2nd to 5th by mistake.

There are many transmission makers (Quaife, others) who make 6 spd seq dog boxes for 300HP cars. Any one of those could be adapted to fit the S2000 but there is development work needed in building the bell housing and the mounting bits and fitment. It's not magic it just requires someone motivated who has the capital to do the development for what is a pretty small market hence why is hasn't been done yet.

If it were me doing the work I'd choose a gearbox that offered a wide range of configurations (dog box, syncro, H, sequential) and build the kit for it universally.

http://www.quaifeamerica.com/transmissions/rwd/15g.htm for example. Note you are talking about $20K all in for this d-lux tranny which is more than what most of our cars are worth and hence a bit rich for club racing.

 

see thats the thing this dogbox that is getting designed right now will go into your stock housing for alot less than that.