I decided to buy the Mini-Din -> Din adapters from creative, but I'm wondering if I should buy one or two. I use the SCC-1 and CM-64 for gaming purposes only, so do I really need more than one cable?
For gaming, one is enough. You only need to send data to the synthesizer. Be careful, though. I had four cables, but now I can only find three

Another question, do I need to connect both the CM-64 and the SCC-1 to the soundcard line in separately, with a RCA splitter cable, or does the sound go through somehow?
Neither the SCC-1 nor the CM-64 has a sound-passthru, but simply connecting the outputs from both devices to line-in via a splitter cable is the wrong way to go about it too. The audio signals need to be mixed properly, otherwise you risk overloading your outputs (Now you don't want to damage your CM-64, do you?) or "just" poor sound quality.
Possible solutions are a cheap mixer circuit (just a couple of resistors) as shown
here if you're the DIY type, or a simple audio switchbox (usually a box with 3x2 RCA inputs and 1x2 outputs and then a knob to switch between them) which can be found at most stores that sell hi-fi or consumer electronics. For gaming I seriously doubt you'll need to hear the CM-64 and SCC-1 simultaneously, so the switchbox is probably the most convenient solution.
This isn't really about SCC-1, but I'l ask anyway: Currently I have a Sound Blaster PRO as digital card on my DOS computer, I'm wondering if I should get a better card for sound effects. Any suggestions?
Well, the SB-16 has 16 bit support for newer games and is SB (and mostly SB Pro) compatible. The AWE 32/64 has the same features, as far as "wave" audio goes, but is a less noisy than the SB-16.
I'd say if you can get an SB-16 for free, upgrade. If not don't worry too much about it...