I see where you're going with this.
One refinement I might suggest, rather than making it invisible, just make it really hard to hit and mark it in play as bonus by having it flash or something. Really hard to hit, as maybe, other side of the screen while the main combo stays on the one side? The mapper will mark such beats as optional in the editor, and missing these will not break your combo in play (or display an X). Hitting them should be worth .. the same? 300/100/50, but if these are scattered through your map, a player hitting them all will raise their combo size considerably and get a bigger score.