Assuming multiple, let's say 50, basic availability groups are on the primary replica. Each AG has its own listener.

The primary replica goes down, and all the AG's fail over to the secondary. How should user and application connection strings take into account all 50 Listeners?

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Assuming they are using the listener name then they will be directed to the appropriate node. Once connected, assuming their login works properly they can see and access any database on that node, even if it's not part of the AG. The listener itself doesn't control access, it is merely a redirection sending you to the appropriate node. Since it's a basic AG, this will always be the read/write node.

You could get into complications if some of your availability groups failed over and others did not, but you probably don't have that issue.

As for logins, just make sure that the SID's are the same on both nodes for the same login (or use windows logins/groups) and you should be ok.

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