Dot Clock specify the SH2 speed, at 4 the SH2s run at the same speed as the console, at 2 they run at half speed. something like that.
Slave SH2 speed is just what it says, the speed in percents that the secondary SH2 runs at.
Both are hacks according to the readme files as many things are not emulated properly. And of course both will cause the emulator to be marginally slower.
SH2 instruction numbers also affects compatibility (higher number - more speed/less compatibility) but I'm sure that the default option is the one offering the best compatibility at the moment.
Infact, if you remember the jingle of the Saturn Bios, then you know that in SSF, its not in synch with the audio, not even with auto frameskip. Because the emulated cpus are not fast enough to render the screen fast enough. But set the Dot Clock to 3 and it will be in synch - the animation speed will slightly go up.
If you have a mammoth system with no slowdown, I think it's safe to say that dotclock 4 and slave sh2 100% is recommended to get the best emulation.