Should scientific theories be understandable -- or at least, aim at understandability? Of course, the term 'understandable' is vague and/or ambiguous, perhaps so much so that this question is some combination of pointless and unanswerable. But let's suppose the concept of understandability (or, equivalently, intelligibility) is sufficiently determinate.
One might think that understandability is not a standard on scientific claims. Sure, it's nice when we can have it; but as certain physicists say, 'Nobody really understands quantum mechanics.' On this view, evidence can justify a theory to a sufficient degree to motivate acceptance of that theory, even if that theory is (in some sense) not completely intelligible.
I don't know what the answer to this question is. But I was recently struck by a similarity between the mechanical philosophers of the middle 17th C and the logical empiricists of the early 20th C. In The World, Descartes says he will describe a universe that only has properties that everyone, even the dense, can fully understand (viz., the shape, size and motion of matter). In "On the Grounds and Excellency of the Mechanical Hypothesis," Robert Boyle claims that one of the advantages of the mechanical philosophy over that of the Peripatetics and the Paracelsian chemists is that the mechanical philosophy only uses terms understood clearly by everybody. The idea is that the word 'cube' will call up the same idea for everyone, whereas 'substantial form' (Peripatetics) or 'active principle' (Chemists) will not. Just about everyone can agree on whether a particular thing is cubical or not -- we will enjoy less agreement about whether a particular substance contains an active principle or not... or about what an active principle is, exactly.
What I now recognize is that certain aspects of logical empiricism have very much the same spirit. For Carnap, Neurath, and other logical empiricists, one of the primary aims of the language reforms they proposed was to guarantee the intelligibility or understandability of sentences that aim to state facts. Neurath proposed the adoption of a 'Universal Jargon' that was supposed to be a refinement of everyday language; Carnap proposed various types of languages at various points in his career -- the language of sense perception was the most fully developed in the Aufbau, and the language of middle-sized dry goods was preferred after that. Why these languages? Because, in each case, such sentences were supposed to be the most paradigmatically or obviously meaningful sentences; if (e.g.) everyday language is not meaningful, then nothing is. Furthermore, these sentences mean the same thing (or close) to all competant speakers; Philipp Frank, for instance, embraced such language-reform projects in order to counteract the Tower of Babel-esque proliferation of jargons in various scientific sub-disciplines.
I think further parallels between the 17th and early 20th C philosophers can be tied into this issue: both groups want to unify science (though in different ways, I think) and to eliminate the excessive metaphysical speculations of their respective times. I think the impetus toward intelligibility, in both cases, drives (at least in part) these other programs.