Suggestion #1 seems far too easy. If the cultists can rattle off all their discoveries from the start, what's to stop them from getting all their runes within in the first twenty minutes?
As for Suggestion #2, I'm not necessarily against the number of cultists scaling to meet the player count, but I'm not sure it's that important, seeing as the cult can grow exponentially...
I think the main problem with cultists is that of every antag on Paradise. Someone invariably jumps the gun and bungles it, thus raising the Alert Level to Blue or higher. This allows Security Officers to search indiscriminately, which they will do if someone so much as looks at them funnily. On a less-populated station, this wouldn't be an issue. Security would be less-staffed, and it would be much more possible to catch someone alone, etc. The solution, I think, isn't to buff antags but to increase the amount of external dangers. I played janitor once, and the experience wasn't "Janitor... IN SPACE!" or "Janitor... WITH MAYHEM!" It was merely "Janitor-With a Pimpin' Ride." It was a soothing experience, certainly, but hardly escapist. If things are running THAT smoothly, I think something's wrong.
Of course, this opens up a whole other can of space worms, which no doubt merits its own topic.