Well, I can't tell from your description what the mode shape of the lowest resonant frequency will be (which is basically what you are asking). It sounds like a job for FEA, but the fact that it is submerged complicates matters - I guess one would have to use computational fluid dynamics. If I could see a drawing of it, I could probably give you a good guess. But since you say the stiffness is "symmetrical", it may be hard to tell. The fact that the housing is football shaped (ie elliptical) suggests that the added mass effect of the water may be lowest in the direction of the "long axis", so all other things being exactly equal (questionable) the lowest frequency would be in the "short axis" direction, although there might not be much in it. Blevins, in "Formulas for Natural Frequency and Mode Shape" has a section on calculation of the added mass for various sections, including circular and elliptical, and some general comments, so this might be of some help. But the propellor will come into it too, and the major direction of vibration may be more influenced by excitation and turbulence/wake effects etc etc - all in all a very complicated problem.