As far as I can tell, we only save 1 SoS doing Snowhead/Ranch/Fortress without bombchus. Meanwhile, that costs us 19 bomb hovers, ~65s. A SoS is ~25s, and SoS+bomb shop is ~45s. Add that to melting the ice and taking the stairs, and I think you've got a fairly large time deficit which won't be made up through rupee collecting savings.
BTW, a dedicated trip to the Bomb shop (ie, warp in, go to bomb shop, warp out) costs ~63 seconds, while a bomb hover costs ~3.5 seconds. Thus, as long as you use all 20 chus, a dedicated bomb shop trip is worth it.
On a 100% related note, as I make mild amounts of progress on cycle 3 of the 100% run (there's SO MUCH to do), I figured I'd take a look into what we actually need for the 4 dungeons, which will be taking up a lot of the cycle and largely determine how the cycle will be structured. And what better way to find the ideal route through a dungeon than to TAS it. So I give you the first of these, ie, Stone Tower.
Part 1:
http://www.youtube.com/watch?v=n-Wa1ONgAo4
Part 2:
http://www.youtube.com/watch?v=1AN-fsVYAUg
Things of note:
--With a bit more judicious bombchu use, we should be able to get it down to 20 chus and still not have to do any bomb hovers. This means we can stock ourselves up to 40 chus before Ikana and not have to warp back to the bomb shop.
--Fire Arrows are needed, so STT must come after Snowhead.
--Elegy of Emptiness (and thus Mirror Shield) must be gotten before you do the east wing of the Inverted Tower.
--takes ~9hr game time (~3hr slowed game time)
--Using Fire/Ice Arrows on Twinmold isn't faster than using the Giant's Mask. Since Ice Arrows are used nowhere else, STT>GBT has no downside.
oh, and while I was doing this, I found this
http://www.youtube.com/watch?v=rPbUZKe1FIo
You can watch the losslessly encoded version here, but it's not what you'd think
http://www.youtube.com/watch?v=NAjs31YeHj8