Myrion, there should be a tile for each orientation so you shouldn't need to rotate them. The tiles weren't meant to be rotated, so I would strongly advise against that. (The pixels would be all wonky). You could get away with vertical and horizontal flipping on some tiles, but you might wind up with some weird tiles that way.
I know the Hex Kit folders can be a bit crazy, so you can always download the original folder just to confirm. The names should be the same regardless of if they're in the Hex Kit or in the regular Pixel Hex Tileset folder.
If, on the off-chance I'm missing something, let me know and I'll get it added into my next update.
Thanks for your support!