They don't go cloudy.. all that happens is that the clear doesn't give as flat a surface as the glass and so you get a slight rippling effect over the scores if the windows are sprayed.
It wont make hardly any difference to where you have the chrome coming through.
If the glass is flaking then it will only get worse.. slowly over time the edges lift just a little bit more and bits start to drop off. In time you will have no choice but to clear it but by then the damage is a bit worse... its something you are going to have to do anyway, so you might as well do it now to retain more of the artwork.
It doesn't have to be a really thick layer.. I know products like " Triple Thick" give the impression that its like spreading jam but its not really.. only a thin layer is needed.. its there to hold ALL of the silk screened art together as one piece. Therefore the whole lot has to drop away as one rather than bit by bit.. the good holds the bad on so to speak.

But... DO NOT use  any polyurethane based clear for this.. it goes to a brown tint over time ( same as an EM playfield)... the stuff Playwell games sells is just P/thane - steer clear. Personally, ive never used Krylon Triple Thick.. every glass ive ever sealed has been done with Acrylic clear