Beholder I: Is the Dwarf on level 5 the only possibility to do so? Can I somehow use the clerics raise dead spell on bones?

Beholder II? Same question: Is there someone able to resurrect my carried bones?

For Beholder 1, yes, the dwarf is the only one who can resurrect them. They'll need to be full sets of bones, not skulls or femurs.

For Beholder 2, in the entry level of Darkmoon (where those creepy priests 'welcome' you) there's a secret wall that leads to a big ankh. From there you can take another teleporter to another ankh.
Each ankh resurrects one of your party members or a set of bones up to 3 times.

There are 2 ankhs in EoB 2 game but the second one is exhausted, this is become evident when you try to use it.
In other words there are only 3 resurrection, but there are only 2 NPC bones and plenty of raise dead scrolls in addition to cleric's own capabilities.

That only works on (non-elven) party members. The sets of bones in your inventory are objects, not party members, so the answer is: No, it doesn't work.

https://www.youtube.com/watch?v=w4aLThuU008

Hah, I never knew one of them is empty. Interesting.