The portals are removed for everyone to see and use, it is no use for people to go to check on alts, mains etc. They will not be there, you can not access or see them.
When the portals were removed the system was changed so that the specific portal needed for a quest would show. Once the quest is complete the portal is gone again. Occasionally there are quests where the portals do not spawn, these are bugs. Bugs should be reported in game.
I have gone through Legion on several alts since the change (not a mage) and all the portals I needed including the Dalaran crater for the Paladin order hall appeared. It is a pain in the posterior when things don’t work and you have to get there using other means.
I would recommend any mage learns the Dalaran crater purely because it is great for putting down at the end of a raid and catching out half your team and sending them to their possible death 
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Summary of how to get this:
Fly to Scarlet Halls (right hand instance). Normal mode.
(Optional) Grab 2 quests inside: Just for Safekeeping, Of Course & Rank and File
Slay everything (at least 50 for the quest).
Make sure you kill the final boss (Flameweaver Koegler) fast and stand infront of him to block him burning his books.
Hand in 2 quests.
Loot book from the shelf just inside on the right. (If you look backwards towards the door, it’s just on the left)
Learn Ancient Teleport: Dalaran.
Go to regular Dalaran
You can now buy one copy of Ancient Tome of Portal: Dalaran from Endora Moorehead (in the room to the left of the Violet Citadel steps).