If you're wondering why there's exactly 12 (+ 1 for the Higgs?) fields, I cannot answer that question and it's one of the open questions in current theoretical physics.
When we have particular constraints (e.g. known energy) that constrains the space of possible waveforms. E.g. when we talk about there being an electron in an orbital around an atomic nucleus, what we actually mean is there's a waveform. of a particular shape around the nucleus.
Are you asking why we only ever see waveforms corresponding to whole numbers of electrons? That's the "quantum" part of quantum mechanics; certain values are quantized (e.g. electric charged). I don't have a good intuition for why that's so though, except to observe that the time evolution of a system preserves this quantization, so there's no way to ever go from having one electron to having half an electron (for example).
A final answer would be boring..... WHY is a fantastic question - it's just not something pure science can answer with finality, only layers until we get to an unknown.
The number of waveforms isn't finite by the way. There's a fundamental waveform for every momentum (which can be any real number) and for every number of particles (which must be a positive integer).
I'm not quite sure what you mean by "orthogonal" as the mathematics involved is not simply linear algebra.
Edit: from what I can understand about the formation of the Standard Model from the Lagrangian, the domain restriction which makes the elementary wavefunctions elementary is wavefunctions which evolve over time (according to EM theory) such that when viewed as particles, their motion is compatible with QM (or relativity?), and that there are only a finite number of distinct wavefunctions which are needed to span this space. Is this roughly correct?