In general yes, if you created a NodeJS projects, with Docker, and a database in Wappler, then on Deploy your database schema generally gets updated, however I often use Navicat to make schema alterations, and on deploy they do not get overwritten in my experience, but I hardly use the database manager part of Wappler in general except for refreshing my schema, when i make changes outside of Wappler.
Look at your Wappler project settings for the remote target, this will give you 4 pieces of information to need to connect to Navicat or any other external database application.
IP Address/FQDN of the Docker container
Port Number
Username x 2
Password x 2
One is the root username and password, where you use the username root
The second is a user type username / password combination so you could set different privileges for it.