So, I've researched for a value that indicates the game difficulty. I'm not sure if there is a single value that controls it, but at least I've found the values that affect 4 distinct difficulty aspects:
SystemID GBA
03A3A0 w u 0 EWRAM score
03C121 b u 0 EWRAM max enemies
03C122 b u 0 EWRAM everyone speed
03C123 b u 0 EWRAM spawning rate
03C124 b u 0 EWRAM currently unknown
These values increase when the score increases. If you poke the score address to a bigger value, the following 4 values will change according to it. If you lower the score again, they won't change, suggesting that there could still be a master value somewhere.
Also note that these 4 values sometimes get temporarly lower...
Edit: getting the score to 990 or any higher number gets the same values. I suppose this could be considered the score required for triggering the maximum difficulty.