Well I can't help much since I have basically no PS2 and few PS1 knownledge. That you didn't find pointers multiple of 2048 means nothing in your case, first the pointers could be sector aligned instead of byte aligned (in which case they'd be disibislbe by 1, not of a great help), and second, I have no idea how big are the sectors on a PS2-DVD-ROM. I know the sectors on a PS1-CD-ROM are 2048 bytes, but that means nothing for the PS2-DVD-ROM.
However, the sectors are very unlikely to be smaller, they should be same size or bigger, so if the sectors were bigger and the pointers would be byte aligned, then they could be divisible by a bigger number, but also 2048, so you'd have found them.
All I can say is that with my long experience of hex hacking (soft of), you can see pointers obviously when you see a large chunks of numbers going gradually up. This is normally rather obvious to the eye if a row in your hex editor is something like 16 or 32 bytes.
Also, I can assure you that you are not in the easy part ! Chacking a virtual file system sure is extremely hard, I haven't done that but I can tell by experience that it won't be easy, especially if they used compression and/or encryption of their data, in which case you'll need to find the ASM of the code decompressing/decrypting it.
However there's some hope, this
translation has been released recently, and is by the same developers, so there is a tiny chances they used the same file system. I can't checked my AIEM disc right now cause I'm not home, but if they use the same file system, then you should hack the authors of this translation if they managed to crack it, and then you'll be able to use their knownledge for your own translation.
I am a huge fan of the Atelier series (well, at least the first two Eternal Mana games as they're the only two I could find so far), so I sure hope you'll be able to translate the game ! Cheers up.