How are water slide decals normally applied to clear bodies?
 

Are they applied on the INSIDE of the body and painted over?

May windows be also blacked out or dark-tinted by spraying the inside of the body?

There is a way to put them on the inside. Once you take it out of the water gently slide the decal off and flip it over then put it back on the carrier paper and gently slide it around on the paper then you can put it on the inside. There are also decal solutions for this at lhs that stock static scale models. Mr mark softener is a good one that comes to mind but you need to put this on the decal after its in place. Hope this helps some

Put them on the outside and spray a coat of clear auto paint (acrylic Lacquer) over them