The pet charm rewards from Warlords content will be significantly reduced, but not eliminated completely. https://t.co/RDXbO1nPey— WarcraftDevs (@WarcraftDevs) March 23, 2016
Come Legion, WoD content will no longer reward the same number of Pet Charms as it does today. They'll be reduced but not completely removed.
For those worried about not being able to obtain enough charms to purchase pets, toys, and other consumables from the pet vendor(s) -- keep in mind that it's likely that the Pet Battle quests and dailies in Legion will also reward Pet Charms.
It wouldn't make sense if Blizzard cut off our supply of charms yet still sell items using that currency. They could change the currency altogether, but that just seems like a hassle and a disservice to those that continually completed WoD content just for the Pet Charms.
It would make much more sense to simply move us to relevant content by rewarding more charms from Legion quests than WoD quests.
So if you don't have all the pets or toys yet, and haven't stocked up on Pet Charms, don't worry. Legion Pet Battle content will probably reward charms (not officially confirmed yet). How many is still unclear, though. More or less than WoD content? About the same? We'll have to wait and see.
For the nervous (like me!), perhaps completing WoD content and saving Pet Charms now isn't such a bad idea though... ;)