I just tested this, and I got the same result. The one exception is that in the Beta version of the Evernote Web editor (not the Classic version), the table does not disappear: the material in the table is centered, but the table as a whole remains on the left. The same thing happens with making the text flush to the right margin, or justifying it (in the Windows program).
So it does appear to be a bug. May I ask why you want to do this? Generally speaking, although the editor functions of Evernote are improving in the Web version, I doubt that it will ever be a truly sophisticated text formatting tool. It is meant for taking notes (and for storing materials online), but not for well-developed writing projects, which require a real word processor. In my opinion, at any rate.