Many creatures lack ranks in skills, even vital skills like Perception. However, even a creature with no ranks in a skill typically has that skill, with 0 ranks, and can use it untrained, just without the bonus of adding their ranks and possibly a class skill bonus to the roll.
The synthesist's eidolon, however, has no skills, which is a bit confusing. Does this just mean that the creature can't put its skill ranks anywhere (or at least not into any skills-- I'm not aware of anything like the 3.5 Barbarian literacy system in Pathfinder, but there might be non-skill places like that)? Does it mean that the creature can't make any skill checks, even those normally usable untrained (this would be similar to what it means for an animal to 'not have the physical ability to perform certain skills')? Is it somehow equivalent to not receiving any skill points (this seems unlikely, since skills, skill points, and skill ranks are quite separate mechanical constructs)?