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Hello Jackson

I posed this same concern to George Huxtable several years ago.

His answer was that it did not affect the observation. 

After puzzling it through, I agree with George. 

Unless your window suffers from waviness or other pronounced defects, the angle on the inbound ray of light will match the angle on the outbound ray of light, after passing through the pane of glass.

To verify, subjectively, that the window is 'good enough', just observe distant objects using your mark one eyeball.  Wobble your head about.  If the distant objects do not jump about or waver, rather, they retain a coherency, then your sextant observation will be just fine.  On the other hand, if the objects or scene is distorted, then the observation will likely be affected.

In general, window glass is soda lime float glass, which indeed has parallel surfaces.  So in general, therefore, your sextant observation will be just fine.

Brad