Some agricultural crops are normally harvested before the plant produces its seeds, or before the seeds mature. For example, hay is mown when the leaves are largest, before the seeds ripen and the stalks turn to straw. But for productivity it is important not to keep harvesting the same plants year after year, but to allow some of them to go to seed so that new plants can grow. Thus some of the crop is left to stand for seed instead of being harvested.
I would advise, that if you have a good kind of Colly-Flower that blossoms early, and has large and close Flowers, to let some of the forward Plants stand for Seed, carefully tying them to Stakes, that the Winds may not injure them. When the Seed-Vessels are full grown, and the Seeds within them are perfected, cut off the whole Stalk, and let it dry in the House before it be thrash’d out; for it is not necessary to leave the Seed upon the Plants till the Pods are dry, lest they open and shed.
Richard Bradley (1718). New Improvements of Planting and Gardening, p. 148. London: W. Mears.
So the clown’s joke in Measure for Measure likens the “houses of resort” (brothels) of Vienna to an agricultural crop, where some of it (in the suburbs) is harvested, but a proportion (in the city) is allowed to go to seed for the production of the next year’s crop. There is also a rude pun on “stand” (meaning “to have an erection”) and “seed” (meaning “semen”), alluding to the activity in these houses.
I doubt that Shakespeare can have intended a pun on “gone down” as the sense “go down, v. perform fellatio or cunnilingus” is much too late—Chambers Slang Dictionary says “(1910s+) (orig. US)”.