A good thing to consider is where the harmonic oscillator potential comes from - fundamentally it comes from taking a taylor expansion about an equilibrium (thus harmonic). According to Zee's book this is also true in QFT. The point is, \omega, is not some arbitary frequency - it relates to the second derivative of the potential about an equilibrium, evaluated about that equilibrium (I think you also have to assume a stable equilibrium to get the right values and functions out)
The point is, the Harmonic potential is an approximation that is liable to change. This is especially true in something like the vibrational spectra of a diatomic molecule, where the potential can change based on the binding, and the equilibrium position too! Then the functional dependence of the "zero" point of field can become something very physical. Of course, as one can only really measure transitions between energy levels, actually deciphering this effect is somewhat difficult - and clearly the approximation to a harmonic oscillator is what's at fault if anything particuarly interesting happens.
For a "fundamental" oscillator like the Quantum field, it depends whether you think it's fundamentally an oscillator or not. If it really is and \omega is a true constant, then it doesn't matter in the slightest. If it isn't, and \omega is actually a function, then potentially it could. Someone may no more on this.
The relationship with the uncertainty principle, specifically with the energy-time uncertainty, states that
\Delta E \Delta t ≈\hbar (or was that \hbar / 2 ...)
The question is, what the time actually means - turns out it's the lifetime of the state - for a state of well defined energy, like those that you get from treating the time independent Schrodinger equation), they don't evolve in time, and hence \Delta t is infinite!, and therefore energy is arbitrarily well defined. Of course, this is telling you that states of well defined energy don't physically exist. Or more precisely, no real particle exists in a state of well defined energy, otherwise it can never evolve, and thus could never have got into that state in the first place! However, they are very useful, for dealing with a whole load of systems for which the energy is reasonably well defined (or long lived states, on the order of quantum oscillation of the state, which has scale \hbar / E, so is not necessarily very long at all!