Elliptical polarization and waveguides
Let's directly answer your questions, first, then address your misconception:


  So, I'll say that waves in waveguides are simply linearly polarized


That can't be the case. How would you, in a round waveguide, like a circular tube waveguide or, very prominently, a coax cable, satisfy any boundary conditions with a linearly polarized wave (in cartesian coordinates, at least). 

You can very well have a waveguide with e.g. a circular polarization; for example, when you open a satellite dish feed (satellite TV is circularly polarized), there's parts of the waveguide system that are linearly polarized (because that's easy to pick up with a monopole) and parts that are circularly polarized, and there's the transition between the two.

So, nothing to see here: wrong claim, can't be justified.



Polarization is something that you define from the direction of the E-field. 

In free-space propagation, that's easy: at any given time and point, a plane wavefront will have exactly one direction of the E-field.

It doesn't work if you have a mode propagating in your waveguide that has more than one half-wave width. Higher-order modes usually can't be assigned any polarization at all; not even an elliptical one. The concept polarization doesn't apply!