There are issues besides merely diseases.
Also, Ax getting sick in book 29 was an andalite disease.... which should actually not be a disease but a problem that andalites face. From what we are told, the tria gland collects disease organisms into itself (how this is biologically possible is unknown) and when it ruptures (due to inflammation), the diseases are spread throughout the body and Ax proceeds to die, since the part affected most quickly would be his brain (tria gland was at the back of his head).
This actually doesn't make sense, since;
Morphing does not transfer disease unless it's a genetic disease.
Morphing would have sent the tria gland into Z-Space; the progression of the organisms would have either be held still and or killed, since morphing does not 'return them' back.
But more to the point.
One issue that should have been noted is the indifference in gravity; the reference is only made once to Erek who says that the Chee were creaed in a gravity four times stronger than Earth's.
For the hork bajir, and the andalites however, the gravity difference should have been noticeable. Hork Bajir live in a shattered planet; it's gravity would have to be a lot less than a full planet's. Unless the HB homeworld was so huge that even when shattered, it held a gravity stronger than Earth, the majority of the aliens in the series should have problems with just day to day walking.
And if you say they may have lived on a world whose gravity was stronger, therefore, they would be unaffected by earth's weaker gravity, there are side effects of reduced gravity; mainly that there is reduced load on the bones, which results in excess bone being shed to conserve the body's energy. Translated; the aliens would have gotten weaker over time. A visual example exists in the pixar movie, Wall-E. The humans have lived so long in an artifical gravity that they've all become fat, and their bones are barely able to support themselves; they have to use hover chairs to get around.
Unless the Yeerks altered the planet's gravity (which I would have think the rest of the world would have noticed) the aliens should probably have encountered some problems.
Furthermore, the argument that diseases wouldn't survive constantly in an unexposed alien body sounds right, except that this simply gives the aliens a ticking timer; they have at best, extremely high resistance to the disease at first, but with continued exposure and subsequent success over the bacteria, bacteria mutates. Diseases that andalites, hork bajir and yeerks/taxxons may have been extremely resistant to at first would eventually mutate due to their constant exposure to a foreign body; bacteria adapts much quicker than normal evolution, and this is why when you take anti-biotics, you are asked to complete the course; failure to do so may allow the remaining disease organisms to become resistant to the anti-biotics, such that the next time they attack the body, Ax may just collapse and die.
Mutating diseases is why the world is still plagued by illness; this is why when someone suffers an illness in childhood which is later controlled, when it breaks out again years later(such as when they are old and have a weakened immune system) the effects would be vastly more significant than the original disease.
And 3 years is a lot of time, time which they are spent pretty much in all over the world, in other planets, touching foreign aliens and morphing animals. Any of them could have fallen sick, and really, if they had, that was pretty much game-end for the animorphs. Ax being sick can't be cured; there are no andalite doctors. any of the animorphs get sick, and they go to the hospital. subsequent anomalies with their blood reports will force the yeerks to discover who they are; if they decide not to get a doctor, the affected animorph may very well die.
Aside from the gravity and the realistic possibility of disease mutation, there is also the problem of the atmospheric difference. Someone brought up that earth animals are hardy and can last in eviroments they are not built for; this usually only applies to habitat; no animal has been built to survive breathing a completely different form of air than what it was evolved to breathe on. No animal (ithout genetic manipulation) ever will. It would be like asking a human to start breathing nitrogen gas and still be able to walk, talk and perform as if he were breathing oxygen.
Animals on a planet are built to survive typically on that planet alone. And some rare cases exist where the animal is built to survive in a very specific type of habitat; this is why beached whales die despite being created on earth; they were evolved exclusively to live in an enviroment where their mass would not kill them. A beached whale is so heavy on land that it cannot actualy move itself.
Ultimately, it just makes it so that earth seems to be a natural 'safe zone' for all aliens; they will never have to worry about dying from anything other than a twitchy tail blade or dracon beam/shredder fire or starvation. And of course, wild animal attacks.
