I'm primarily a Shadowrun player, but also an Eclipse Phase dabbler, I'd say that part of the reason for cyberpsychosis in Shadowrun is the "unnatural" state of being and Essence loss (though this is not necessarily the causality). In addition, cyberpunk tends to be about the consequences of actions, and it almost logically follows that changing your body changes your mind. As for Eclipse Phase, there is no penalty for two reasons; first there's no transgressive element to augmentation as in Shadowrun. Second, if you look at the people in Eclipse Phase, a lot have switched bodies, and the average psychological profile in Eclipse Phase is looking at someone who has potentially been in hundreds of different morphs (though practically they probably haven't), or at least switched bodies once, so cyberware isn't as big a deal.
Of note, however, are a couple things:
Part of my rationale for Shadowrun cyberpsychosis involves Essence, which is in my opinion contrary to the original cyberpunk idea that modifying yourself physically directly alters your mentality when one considers that different grades and types of cyberware are more or less invasive. For instance, Delta-grade bone lacing probably won't turn anyone into a raving sociopath, so it stands to reason that standard bone lacing wouldn't either, even if it pushes their Essence low. That said, Essence reflects the amount of psychological impact that cyberware or other events in a character's life has (though not directly; it's more of a physiologically tied thing as well) so it does make sense that low essence characters might become psychotic.
At the risk of going on a tangent, I'm going to look at cyberzombies in Shadowrun; the spirit of someone with a lot of cyberware (or maybe just a random spirit, there's wonderful amounts of ambiguity) bound to their body by powerful magic, cyberware, and medicine (well, the medicine just keeps the body working). If the loss of Essence is so severe that it rather literally causes death and requires a trip to the metaplane of death to prevent the loss of the poor sap on the operating table, it could stand to reason that cyberpsychosis is the same process (if you will) of the individual, much less distinctively so than an Awakened mage, a low-Essence individual being impacted by the loss of connection to the natural state.
As far as Eclipse Phase, I think there's a number of reasons there aren't major impacts from cyberware there; first there's no Essence system in place, "natural" is whatever your mind is acclimated to at the moment, while Shadowrun had a very overt layer of mind adjusting to natural body. Second, the "basic" packages for cyberware and bioware that every morph in Eclipse Phase but the bioconservatives would run 1-3 Essence as standard Shadowrun equivalents, if we assume the cortical stack is relatively unintrusive, so we just really count mesh inserts (equivalent to a decent commlink + image link + datajack [to simulate the direct neural interface] coming to .4 Essence), effectively Age Rejuvenation, though this doesn't see Essence penalties in 4th Edition, probably a Pollution Tolerance genemod, adding .5 Essence to reach .9, probably a Microgravity adaptation though that's not explicitly stated which would add another .5 essence, but ignoring that we can add Basic Immunity immunizations for several diseases (.1, times however many diseases you want gone; probably like ten or so, but let's say .3 Essence), for 1.2 Essence rather conservatively, and that's for the basic package if we leave out morphs that are engineered explicitly to do things that normal humans absolutely cannot, rather than just being "better" humans. This also assumes that you're not doing stuff outside Shadowrun's rules; cortical stacks, for instance, are not included in my tally. Now, admittedly, EP would probably be using Betaware or better relative to Shadowrun, but there's a lot more stuff on most morphs than I listed here; PC's tend to get more mods, making them easily in cyberpsychosis areas if they do packages like I've seen.
Finally, note that there are Exhumans in Eclipse Phase who are pretty much near cyberpsychosis, so it's not entirely absent.