When I first got my PS4, I made an account, registered it in USA and started playing. A few weeks later, I made another PSN account on the same PS4 with region UAE this time.
Will the PS Plus UAE subscription code work on the UAE account or will the PS4 still think its USA based?
A PS Plus subscription is shared between all users on that account's primary system. As long as your PS4 system is the UAE's account primary system, your US account can play online and access all games normally.
As the PS4 has no region lock, the only thing that matters is primary/secondary system. Check the PS4 User Guide for more information.
