Can a magnet cause a microwave oven to unsafely radiate energy?
If I understand correctly, this was due to the deviation of the electro-magnetic (EM) radiation beam from its intended target, as influenced by the speakers' magnets.


No. There's no "EM radiation beam" here. There's an electron beam. "EM radiation" is radio waves, light, x-ray, in short: all the electromagnetic waves. 

Your CRT works by accelerating electrons, which very much act like particles and not like waves at the scales and energies involved.

So, what happens is that these charged particles are subject to Lorentz force. You should probably read the wikipedia article on that, if you want to understand how the deflection coil in a tube TV works (or why your speaker magnets have that effect).


  If I further understand correctly, the magnetron of a microwave to produces a beam of EM energy 


Nah, not really. The magnetron is a cavity in which a wave is kept resonant and amplified through a strong magnetic field. Not a beam, at all! 


  which is directed at a reflector or scatterer, 


Since this is a wave, and doesn't behave like a beam at the sizes of microwave ovens: Be a bit careful with your wording; this is all wave phenomena, so while you can reflect the e-Field of the wave, this is not a "specular" reflection like a laser pointer on a mirror.


  and then into the cooking cavity which attenuates the energy through notch-filtering and corner-wave traps.


No, the energy can't be attenuated. There's conservation of energy. There's just constructive and destructive interference, leading to higher field strengths in some places than others.

The energy in the interchanging electric and magnetic field is then absorbed by molecules of the food you're intending to heat and converted to exactly that: heat.


  Is the magnetron contained within the cavity/[farraday ]cage, and if not, can the beam 


not a beam! 


  of EM be deflected such that it could escape or deviate enough to emit radiation into the surrounding space?


sure. We'd call that opening then an antenna. 


  (If the magnetron should be situated within the containment structure, are there regulations stipulating this?)


No matter where the magnetron is located, the amount of energy that a device can emit is draconically regulated by national and international bodies; in the US, that'd be the FCC; in Germany, the Bundesnetzagentur, in UK the OFCOM, and so on. 

Generally, microwave ovens aren't allowed to emit any significant amount of EM radiation, especially not an amount able to hurt bystanders.


  This situation is more practical than hypothetical: We have a neat kitchen gadget with a strong (rare-earth, I think) magnet on its base, designed to hold itself to an oven door with substantial certainty. Attaching it to the oven isn't an option, so it's currently on the over-range microwave oven. In a moment of analysis, I realized this may be a poor choice...


A static magnetic field should have no adverse effect. You can verify that by adding a static magnetic field component \$\mathbf B\$ to Maxwell's equations and realize that for the static component, \$\frac{\mathrm d}{\mathrm dt}\equiv0\implies \mathrm{curl} (\mathbf E) = - \frac{\partial}{\partial t} \mathbf B = 0\$, which simply means that the E-field isn't bent by the static magnetic field, and hence, the wave can't take a different direction.