any idea if the NT-01 could be modified orientation-wise
The 'wings' appear to be removable
Yes, they are. It comes with a set of 'wings' for LGA775, and another set for AMD. But the wings can only mount on the ends, not the sides (i.e. you can't move the wings to the 90-degrees adjacent edges). For LGA775, the mounting holes form a perfect square, so this doesn't matter - you just rotate the whole cooler assembly, wings and all. It mounts in any of the four orientations.
an i945GTm-VHL based-system
Um, I may well be wrong, but I thought the mounting hole/screw spacing pattern for those AOpen MoDT mobos was completely non-standard (i.e. I think that only the included AOpen cooler will fit the mounting holes). So you'd need to fabricate custom wings for the NT01 in this application. If I recall correctly, each wing mounts to the copper cooler-base with two short and smallish (M3 or M4, I think) countersink phillips-head machine screws. The wings are basically just flat sheet steel (2mm or less thickness) with holes drilled in (some countersunk). It wouldn't be hard to fab replacement mounting 'wings', for whatever hole spacing you want. But you'd also need to figure out a way of accounting for the z-height of the cpu top-surface, which is unlikely to be identical to that of any of the standard CPU form factors. You could use the preloaded-spring mounting screws that Silverstone includes for use on AMD, to solve that, I think.
If I were going to re-build my NSK2400 (built Sept 2006) now, I'd use the mini-Ninja, rather than the NT01. I strongly suspect it would provide better cooling. But perhaps on a i945GTm-VHL, the mini-Ninja would conflict with your add-in cards, so the NT01 might be your best option.