Context: in the body, considered by itself, the human is weak.
Quid vero, si corpus spectes, inbecillius homine reperire queas quos saepe muscularum quoque vel morsus vel in secreta quaeque reptantium necat introitus?
Translation:
Now here is a truth: if you would examine the body, you would find humans very weak. Why, the bite of little flies often kills men, as can an invasion of them, crawling into some hidden part of the body.
in secreta quaeque: I am unsure about this. Tentatively I say that secreta is accusative plural, an adjective with noun force; quaeque I take as an adjectival pronoun modifying secreta lending an indefiniteness to the secret places.
spectes . . . reperire queas: both present active subjunctive. I read this as a conditional sentence about a philosophical point, that might or might not actually be tested.
introitus: I take this in its meaning of invasion, as the joint subject of necat, with morsus.
quoque: means something like even, even the bite, for example.
I think your understanding of quoque and quaeque is correct.
But this is a question. Crudely:
“But if you should look at the body, what might you find more feeble than the human being, whom the bite(s) of even tiny flies, or an invasion of them creeping into some secret/hidden [parts of the body], often kill?”
Note that spectes and queas are subjunctive: this is in form what A&G call a “future less vivid” condition (sec. 516), but really it’s more like a “general” condition (sec. 518):
The differentiation between future less vivid and general conditions is probably less rigid in practice than the grammar books would have you believe. The subjunctive in both protasis and apodosis conveys potentiality. I think it’s best to keep that in mind when reading–to mentally associate the subjunctive with potentiality–instead of trying to classify these types of conditions. (Contrary to fact conditions are a different story.)
Also noteworthy is the shift from singular homo to plural quos. This is an example of constructio ad sensum, aka synesis. A&G 286b:
Thanks Qimmik for the reminder that this quotation is a question. I overlooked that in my struggle to understand the other aspects. I’n general I have a hard time with questions, and especially words like quid that signal questions.
The general condition in the subjunctive was something I didn’t recall studying at all.
I’m glad I got quaeque and quoque satisfactorily. I need some focused practice on pronouns, practice so repetitive that I’ll improve on catching those meanings.
One more point on muscularum quoque: note that quoque is juxtaposed to muscularum, not morsus. So it’s not “even the bite” but rather “the bite of even small flies.” And the position of muscularum towards the front of the clause places the emphasis on the tiny size of the flies, in relation to the human body. It’s hard to convey this with English word order. Perhaps a less literal translation would be called for here: “whom even small flies kill with their bite or by invading some hidden parts of the body.”