Yes, they do affect history.
All characters are vital, as are your decisions about them. There is nothing throwaway here.
You can have sex with the cheerleaders at the dorm with no ill effects. It only becomes an issue if you have sex with them later in the game. i.e. It's not those girls that are consequential, it's the timeline.
What affects the ending of AL (and I am willing to bet in BaDIK as well) is the relationship status with the LI(s) you are pursuing at any given point. The leeway you have diminishes the higher your relationship with them. Before it crosses a certain threshold, you can fuck anyone (including the cheerleaders).
The threshold for Megan and Malissa is reached when you go to the Beach. After this point you can't with
anyone else (not just Hedwig/Angela but Rena, Leah or Ana either) or at best you get the bittersweet ending. For the Rena ending, you can screw around right up to Ana and still get the best Rena ending because you don't say you want to be "exclusive" with her until much later.
I am pretty sure it's going to be similar in BaDIK. i.e. It's likely still "safe" to screw around with the minor HoTs/strippers now - like with Mona in the toilet. However, once you profess a commitment to a LI of your choice, if you screw with Mona after this, chances are high that you'll be screwed - but this doesn't in and of itself make Mona an important/vital character.