A visual system is only difficult if you have to evolve it over generations
The mistake is thinking that the humanoid eye, or any creature's eye in fact, is particularly good. In fact contrary to William Paley's opinion, eyes are a pretty crap design, and as such they're a great example of how "just about good enough" is generally where evolution lands. Eyes are a miracle in the same way as the results of Junkyard Wars are a miracle - the miracle is that it works at all, not that it works well. That's why visual tricks are so effective, because so much of what we "see" is actually our brain filling in the gaps with rather low-quality images. Saccades, blind spots, varying colour responses, bad response to rapid changes in brightness, inaccurate focussing, and so on.
If you aren't limited by this and you can reshape everything yourself, life becomes way easier. You can fine-tune the shape of the eye. You don't need the horrendous bodge-job of cornea and lens - instead you can just use one accurately-grown lens which you can reshape dynamically as needed. You can fine-tune your retina shape, or whatever you project the image onto, and choose the resolution.
And even if you're starting from nothing, the evolution of the eye shows that if you start with a basic ability to sense light and dark on a flat area, it only needs trivial trial-and-error to reshape that area in ways which first produce "pit eyes" and then pinhole cameras, and this has been demonstrated with software simulations. A lens is harder to come up with, but if your natural substance is a thick liquid with some refractive index (as Odo is) then a simple droplet makes a good first lens which again can be refined very easily. Every step of improvement is clear, and would be obvious to Odo when he did it. A few hours of tinkering would be more than enough time.
This even feeds into why he'd have deeper eye sockets with dark areas around them. These reduce lens flare, in the same way as a camera's lens hood. Human tribes living in snowy areas did the same thing by painting wood ash around their eyes. (Again this provides a counter-argument to Paley by demonstrating that intelligent design would produce something better, because the scope for improvement is obvious.)
The only mystery for Odo is that he's limited himself to two eyes. Flies manage to assemble a wide-angle image from multiple eyes, so there's no reason Odo couldn't do the same in principle. Out of universe, of course the reason is clear. :) In universe, we have to assume he's chosen that limit to avoid upsetting the various binocular humanoid species he's living with.
Regarding his ears though, Dr Mora is making the likely-incorrect assumption that Odo would want to accurately recreate human ears. The human ear shape is basically a crappy compromise between all-round hearing and directionality. Without all the various strange folds and flaps, Odo could easily fine-adjust its shape so as to focus sound from wherever he wanted to at that time. Again we have to ask the question of why Odo would choose to emulate the humanoid ear shape and not, say, dogs or owls, and again we have to assume that this is him choosing limitations which help him fit into society. In the world of Star Trek where there are many humanoid species with slightly different shapes, he doesn't have to perfectly emulate any one species - he just has to look "normal enough" to not obviously stand out.