Yes, apothecary shops were reliable sources of reliably poisonous substances from the Middle Ages on. Not that any items on the shelf would be marked "To Kill People," but rather, apothecaries stocked plenty of powders and liquids for other uses that could certainly be labeled "Will Kill People."

Realgar, which we recognize today as a form of arsenic, was one of several options if you wanted to buy something to kill rats, mice, or the like. It was also used as a paint pigment. In fact, realgar was sort of the Kleenex or Band-Aid of the poison world--it served as the "brand name" for poisons in court cases when the actual substance was unknown.

Apothecaries also sold sublimate of arsenic/sublimated arsenic (what we would recognize as white arsenic). The 1380 edition of the gunpowder manual Das Feuerwerkbuch directs its readers that they can buy the ingredient arsenic cheaply from the apothecary! In 1691 Rothenburg, innkeeper Barbara Ehness puchased white arsenic to kill the mice in her home; in 1692, she was convicted of using it to attempt to murder the family lodging with her (including their four children under eight years old). Their horrific sin that drove her to want to kill? The father had insulted her cooking.

Mercury, as quicksilver or as mercuric chloride, made fewer appearances in court records but was still a frequent enough crime-poison that had legitimate medical uses. Charles the Bad (of Navarre) charged an English musician, Robert Woudreton, with the poisoning of any number of Valois rivals. Woudreton purchased mercuric chloride for the task, claiming it would treat his horses' wounds. According to Woudreton's confession, in fact, Charles, in specifically told him that he could easily find the poison in apothecary shops (ostelz de apoticaires) in pretty much any town.

Among the poisons mentioned in court records, there were a few more of the chemical variety (rather than animals or plants), like lead oxide, but they weren't nearly as popular among poisoners.

Just like apothecary shops had a long history of selling merchandise that doubled as murder weapons (or means of suicide), cities had a long history of trying to regulate them. The most common tactic was to require apothecaries to keep a list of every potentially poisonous substances they sold, and to whom they sold it. My people, in Nuremberg, passed their first version of the law in 1496. These laws, as you can imagine, became much more frequent, enforceable, and useful as urban literacy increased and paper replaced the wildly more expensive parchment. From the early fifteenth century, Bordeaux in France had an ordinance forbidding apothecaries from having/selling realgar, arsenic, and other poisons if they were not kept locked up!

For their part? There are even a couple of reports of alert, ethics-over-profit apothecaries who refused to sell poisonous substances to would-be murderers (and indeed, tried to find out whether a purchaser was a would-be murderer). But Shakespeare wasn't pulling things out of the air. Apothecaries absolutely had a reputation for deliberately selling poisons--and, indeed, for administering the poisons to the intended victims.

My apologies for my answer being focused mostly on the late Middle Ages; I hope you can see how the trajectory continued into the early modern era as well.

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