It all depends on the kit. For larger scale aircraft such as smaller aircraft at 1/48 etc., the cabin windows are larger and easier to mask. For larger aircraft at smaller scales, say at 1/72 or 1/144; doing a good job on the cabin windows gets harder.
Take the clear pieces. If you paint the fuselage halves first and then go and install the windows, and put the halves together; you then need to deal with the seams, repaint etc,.
If you install the windows, join the halves and then paint; you need to mask the windows which is a near impossibility.
I've tried various work-arounds like painting a large part of the side with the window stripe color, then installing the windows and then joining the halves; then masking the entire stripe and painting the body.
There are a lot of advantages to using decals. Often the window pattern and sizes are more accurate than the plastic parts.
I personally don't much bother with cabin interiors if they aren't visible, so I don't care if the windows are clear.
Just my 2 bits.
Bill