I noticed that the CN Nvidia Shield version seems to be merged with the GameCube release on the leaderboards. Are there any real speed differences between GCN/Shield? Which one is theoretically faster? There doesn't seem to be a huge amount of documentation on its differences.

There's a lot to unpack. I suggest reading the text channel #any in the channel category 'Shield' in the TP Discord server. The TL;DR is that load times are ridiculously fast. Some stuff is not possible, like BiT and Map Glitch, but the fast loads still go hard in most categories.