I think my biggest thing is that the balance is all wrong for that particular area. The stairs are wider than the warp point, which looks off. Honestly, it'd probably be better off with the stock staircase with a missing centerpiece.
Right, lets address this first, if you look closely you will notice that the staircase is actually two pixels shorter than the warp pad in terms of width, so it is actually smaller, not wider. Though I do admit it could give the illusion of being wider due to the fact it is out of line.
Back to the stairs issue people are concerned with in the programming. Heres how I see it, no need for any special coding at all. The bottom of the stairs will not rise above Links height. Anyone who has tried to walk under a concrete ledge which finishes below their own height will know they have to duck or crawl, so this will not be possible in the game. This allows a simple collision to be made on the line where the stairs break apart, with no issues. The top of the stairs would simply be on another layer, and therefore link would be able to walk both above and below them. As for the hook shot, have it so that link changes to the upper layer has he gets to the top of the first half of the stairs, he is then able to hookshot, giving the illusion of a diagonal.
I think that would work rather well from my own perspective as a programmer.
Moving on from that, I have now finished the Hyrule Castle Courtyard, please observe:
Criticisms are welcome as always. I also do know that the first statue (the wide one on the rock) currently sucks rather badly, and I will be fixing that at a later date, when I can think of a worthy replacement. I have changed the orientation of the main courtyard where you can find Zelda so that the perspective makes sense and has the same feel as in OOT. I am also aware of the lack of a clear entrance on the very right of this area, however because of the way doors work on the castle, portraying one is actually very difficult. It should also be noted that it is the only entrance, and the one you enter through, so the player should have no difficulties in recognising it.