Those "bonuses" from the bestiary are not a racial bonus or the like that the psicrystal gets for being a psicrystal, they are the baseline psicrystal's total skill modifier in those skills (the final number that actually gets added to the die roll to determine the check result). It's not clear where they got those numbers, as the lack of a static number of HD makes it difficult to even attempt to reverse-engineer that part of the stat block, but best I can tell, the only components in it that carries over to an actual psicrystal with a psionicist master are the racial bonus to climb (+8), and the use of Dex instead of Str to determine climb modifiers, both of which are mentioned under the "psicrystal granted abilities" section.
As for the class skill bonuses, that is covered on this page: http://www.d20pfsrd.com/psionics-unleashed/equipment/psicrystals
It only mentions the psicrystal inheriting ranks from the master (note that they also have at least 4 ranks in Perception and Climb, even if the master does not), not other sources of bonuses, such as class skills, so by RAW, they would not gain the +3 bonus for the master having it as a class skill. They do have their own set of class skills, but unless they somehow manage to obtain their own class levels or some other source of class skills, as constructs, their set of class skills is the empty set (all skills are cross-class for them). Having them inherit the master's class skills would be a perfectly reasonable houserule, but would be just that: a houserule, not RAW.