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It all depends on the type of plastic used for your bottles. Most plastics can’t hold solvent based thinners. If it is PTFE plastic, it’s not a problem at all, other plastics may melt.
I guess you have to test it. I used the bottles from Vallejo and they withstand cleaning using lacquer thinners so my bet is they can be used to store the lacquer based thinners. Myself I use empty glass bottles which held coffee milk. Works great, downside is, I have to use pipettes to get the thinner or lacquer based paint out.

There are people that even use index for thinning their paint… But this only works for acrylics, only the water based acrylics like the ones from Vallejo. The Mr.Hobby Aqueous and Tamiya acrylics are alcohol based and won’t react well with Windex.
You also could use window wash fluid for cars. I use it for my water base acrylics and it works great!
If you choose to use Windex, make sure it contains ammonia, as this is the “chemical” which helps you break down the paint.
Make sure you don’t let the paint dry in your airbrush as Windex won’t be able get it out. You’ll have to do a complete strip of the brush in that case.
If the water based acrylic is still wet, whatever you do, don’t use a lacquer based thinner to get it out, it can turn the paint into a goo which is very hard to clean.
As for the other type of paints, you can use their own thinning agents or lacquer thinner. I use lacquer thinner for all of them (except water based acrylics) to clean them out of the airbrush but dilute them with their on thinning agents.

I hope this answers your questions.