The shinespark up towards botwoon? or you mean the wrecked ship? Didn't you go up red brinstar to get to wrecked ship anyway?
There are certain tricks that are pretty crucial to getting a decent time for any%.... getting grapple is a big time sink, you should learn the sparks! They aren't too bad. glitching past the zebetites in MB's room saves you from having to get a million missile packs that you don't have to have otherwise. Sequence breaking to early supers is big too.
The only shinespark I completely suck at is the one where you jump in the air and then launch horizontally from the air. You need to do that to get into the wrecked ship from upper brinstar without the grapple beam afaik. I think I could otherwise do without the grapple (of course, you need it in RBO to do suitless Maridia). I'll have to try to master the horizontal air spark under less stressful conditions!
Just started playing this game again last week. I play very casually at the moment, but I do utilize some of the speed run tricks to get early items.
How I do my midair horizontal sparks is like this:
Charge shinespark, jump diagonally and hold d-pad in direction you want to go. While still holding d-pad, Tap aim up and then quickly tap jump.
However, I've only managed to do the one you're talking about like 5% of the time. Having to fire a shot (to open door) then do the spark adds a new level of complexity. I usually just do two horizontal shinesparks from ground; One across missile room and one across ocean. It's slower, but it's faster than getting grapple.