Moving SQL server 2016 DB's from mirroring to HA
Since you are on standard edition - you will be using Basic Always On availability groups for a single database. 


  Once we move to HA with 1 listener for each DB, will this new configuration be any issue for me?


The only issue that I see is that you have to failover all the interrelated databases together (since your app has cross db calls e.g. joins, etc).

I don't see any other issues except the limitations highlighted here.