Where their hygiene isn't affected UNLESS the bed needs to be cleaned? I don't even know if such a mod exists, Google's not turning anything up, but that would be awesome! I specifically want it to be the pet beds rather than using a custom toddler bed.

have not yet tested, but I take Apartment Life added toddlers to pet bed users.

Well, I did not even know that toddler's hygiene would decay from sleeping on a pet bed. I agree then, it should only decay if the pet bed is actually dirty and needs cleaning.
A lot of my toddlers sleep on a toddler bed I made from the pet bed cushion. Can you believe, I never noticed about their hygiene. I think, that the pet bed only gets dirty if a pet actually sleeps on it though. It never gets dirty when my toddlers use it, and pets aren't allowed on it. Next time I play, I'll check if the toddler's hygiene still decays.

The real thing that makes pet beds not ideal for toddlers is that energy regen is extremely slow. I once had a toddler who was being raised by a vampire who lived alone, so all day while the vampire was asleep the toddler satisfied her own needs using pet beds and pet food. Refilling her energy bar took a very long time, she basically only had time to sleep and eat during the day, whereas toddlers in cribs regain energy very quickly and spend most of their time skilling. I haven't tried modded toddler blankets.

I would not know about toddler blankets, i never had those. But Charity made a mod for the energy gain and can be found here
http://modthesims.info/download.php?t=542654
I do not have it though. It is a BHAV edit. Maybe something similar can be done (certainly even...) about hygiene. I would not know how, but....

I never even noticed that hygiene decreased while in pet beds. I could probably make it not decay, but I don't know how to make it only decay if the bed is dirty.

Oh thanks, that's very useful.