In general, IR behaves just like a beam of visible light. Which is to say, some of it will pass through a transparent sheet of glass and some will be reflected. The more acute the angle at which it stikes the glass, the more will be reflected rather than passing through. However if you are going to use amber glass, the effect of the tinting may be different at IR wavelengths than at visible wavelengths. It may attenuate the IR more or it may attenuate the IR less, no easy way to tell other than by experimenting.
So my feeling is that the only way to tell for sure is to get a sample of the glass you want to use and try holding it between the projector and the remote while you experiment with various distances and angles. If that doesn't work, then as an alternative you might consider getting an RF remote extender system (for example the Radio Shack 15-1950) and placing the IR transmitter end of inside the cabinet with the projector.