Okay so I ran into something pretty interesting with Higan Accuracy (which is horrible in the performance dept, but useful for testing something like this), and oddly enough, I got the exact same 1:1 result on there, same partial black line with most of it missing and the flickering, too, never thought I'd be able to reproduce it on there, so yeah, it's definitely not my Super NT, maybe it's how it acts on certain Snes models?
Higan and the Super NT are based on the 2/1/3 2-chip SNES, which is also the most common type and also what mine is (SNS-CPU-GPM-02, specifically) and probably what Dup84 has.
So, if Higan reproduces this issue, it's not the SD2SNES. It's normal SNES behavior. It's a bug in the hack translation, and it needs to be fixed by the author of the patch. That's still kinda odd since it was apparently tested on real hardware.
Just to confirm, when I patch the ROM, I get an internal checksum of 0xa83d and a file checksum of 0x1320298e for the unheadered patched ROM.
Same location, I'm thinking that the black line is supposed to cover the entire HUD, but instead on both Super NT and Higan Accuracy, I got the exact same results, same flickering behavior where that black line begins. At this point, I don't even know if this can be fixed, or if it's even worth having the devs look into it, I fear it would be a huge waste of time. *sigh* I was afraid of this 
Based on the screenshots on Romhacking.net, it looks like the intended behavior is for no black line at all like on SNES9x.
Edit: It's fairly easy to download and install the jailbreak firmware, run the game, and then put it back to vanilla 4.5, yes?
It's almost certainly not going to fix anything, so I wouldn't bother. I don't have a Super NT, so I don't really know. I guess so?