I have 2 NDSTTs ordered at the same time and have the same problem, but so far only on one of them.
I have now watched the Youtube video, and that is actually what I have been doing to fix the one I have that does this.
I don't think it is file fragmentation, as you would be able to copy all the files off, reformat and copy back on.
This does not work, you actually have to recopy the files from original source (as also shown in YouTube video).
I think it is more likely data corruption than fragmentation myself.
I have both Sandisk and Kingston 1G cards, and they both do it on one of them.
However, I have noticed that if the kids just load a game and play it for hours on end it seems fine, it is more likely to happen when opening a game, powering off, opening another game etc.
Also I noticed that the date on one of the TTMENU files changes (the .SYS file from memory) - not sure if that is normal, only noticed yesterday and haven't looked at the other to check.
(p.s. the one that hasn't played up yet usually gets used by a kid that just plays one game for hours, so that could be why it hasn't failed)
Anyway, would be interesting for those who haven't seen a problem to (back up the files first) start a game, shut down, power up, start a game multiple times and see if it also does that lock up on loading thing.