Yeah loader = kernel. Bad habit from the DS days where firmware, bootstrap, kernel and whatever else all meant specific things but might not be appreciated by those new to it all.
The kernels that moved to SDHC got some speedups in later revisions. With the EZ4 I tend not to use the V1.???? numbers as they were not always updated and it becomes to speak of dates or specific hacked versions.
The saver folder thing is more to speed up the writing the save part back, which is a big part of the delay between turning it on and playing a game. When the save gets written it first has to scan the saver folder. If you have the remains of a few hundred games in there, possibly also some corruption (the save/file system handling code is not the best and you might have seen some, a simple file system check should clear that), then it has to scan the lot and you get to wait as it does it. If you want to see it try taking a game you normally play and putting it on its own on the EZ4.
Two folders is better than all on the root. I am not sure how many games per folder the current EZ4 loaders top out at (originally it was about 80) but fewer tends to be better.
The loading time got improved once way back in the first few versions (it was crazy slow at first) but not really since then. I have not really had a problem with the load times though -- I just loaded a 16 meg game on my SP. From turning on the GBA power switch (with a game already needing to save), finding the game and seeing the boot screen of said 16 meg game was around 45 seconds.
I have 5 pages of games and folders that the EZ4 recognises on the root of it so about 40 files/folders, there may be more but my SD reader is not around right now.