I believe it only has to do with slow microsd cards. The game will freeze sometimes on my Sandisk or 2gb Kingston Japan microsd. But it won't freeze on my 1gb Kingston Japan, or A-Data 4gb Class 6. And...it will not freeze on my DS-Linker or G6 Real/G6 Lite, that all have internal NAND memory.
So no, it doesn't look to be an anti-pirate measure. I would get yourself a fast microsd before Ecclesia comes out though, just in case.