Meaning of "Men are decayed, and studies: she is not." (17th century English)

Read it like this:

Men are decayed, and studies [are decayed]; she is not [decayed].

It is unlikely that "studies" is a misprint, as it appears consistently in the original published edition of 1641 (Google Books):

Men are decay'd, and studies : Shee is not.

This is an example of syllepsis, which in turn is a kind of ellipsis. In syllepsis, one word or phrase is understood differently in relation to two or more other words that it modifies or governs (ThoughtCo, Sylva Rhetoricae).

So here, decayed is understood in multiple ways in relation to men, studies, and (via the pronoun "She") Nature:

• men are decayed, maybe literally (their bodies decay) or figuratively (the idea of generational or societal decline, or of the Fall)
• studies are decayed in a distinct sense. For example, pages may become illegible, books may be lost, and libraries may be looted. Figuratively, scholarship may not be as lustrous as in Ancient Greece or Rome.
• Nature is not decayed.

Why the unusual syntax? Emphasis. Jonas A. Barish, in "Baroque Prose in the Theater: Ben Jonson" (PMLA 73.3, 1958) provides a concise explanation for Jonson's rhetorical choice here:

One of Jonson's customary techniques is to disturb, by one means or another, what we would ordinarily regard as logical word order. The frequent result of such tactics is to promote oddness of emphasis, to undermine expectations of "normal" arrangement; words will fail to appear in looked-for places, and then emerge bizarrely where we least expect them. Jonson's simplest transposition of this sort is to add some element - subject, object, or modifier - postgrammatically, and thus to isolate it. In the statement "Men are decay'd, and studies (Disc. 127), "Men are decay'd" forms a self-contained grammatical unit onto which Jonson has tacked an extra subject. The delayed subject comes as a kind of afterthought, and lends an improvisatory flourish to the remark. At the same time, paradoxically, it completes a rhythmic curve. If we put it back into its "normal" place in the sentence ("Men and studies are decay'd"), we make a more orderly period, and a hopelessly flat one. The same detail that roughens the syntax in one way, by separating elements that grammatically go together, smooths it out in another way by producing a cadence. (p. 192)

Barish then provides several examples from Jonson's plays. For each of these, understand the element that follows to be interchangeable with the subject of the preceding sentence:

A Trumpet should fright him terribly, or the Hau'boyes? (Epicoene, or the Silent Woman I.i.160-161)

when some groome of his has got him an heir, or this barber ... (Epicoene, I.ii.54-55)

Some Divine must resolve you in that, sir, or canon-Lawyer (Epicoene, IV.iv.148-9)

So the unusual syntax modifies the cadence or rhythm of the line. It imitates an afterthought. It emphasizes studies as a thing that also decays.