Why would you put tower speakers in cubbies? That’s like putting Baby in a corner.
Other than it seems like you are already doing it, consider that you are fundamentally changing the way that speaker is supposed to work. If rear ported, you are taking away from potential bass output. By putting it into a cubbie you are also changing the baffle and thus intrudicing potentially significant diffraction for most of the frequency range of the speaker.
If you want to hide them, that is your prerogative... if it sounds good to you, that is what is ultimately important.
Consider though, horn loaded speakers with narrow dispersion patterns an either sealed or front ported boxes that will at least vent as designed for improved low frequency response.