We are currently using direct DB connection to query mongodb from our scripts and retrieve the required data.
Is it advisable / best practice to make the data retrieval from DB as a microservice.
It does until it doesn't :)
A service needs to get its data from somewhere and a database is a good start. If you have high loads you may find that you need to add a cache in the middle see this post from Instagram engineering https://instagram-engineering.com/thundering-herds-promises-82191c8af57d
edit (after comment) generally speaking, a service should own its database and other services shouldn't access another database service directly only via its API. The idea is to keep services autonomous and enable them to evolve independently.
Depending on the size of microservice, that's now always practical since it can make the overhead of having the service be more of the utility it provide (I call this nanoservices). Also, if you have a lot of services you don't want to allow each one to talk to any other (even not via the DB) since you just get a huge mess. The way I see it there should be clear logical boundaries (services or microservices) and then within each such logical services you may find that it makes sense to have more than one "parts" (which I call aspects) e.g. they have different scaling needs or different suitable technologies etc. When you set things this way aspects can access the same database and services shouldn't (and you can still tame the chaos :) )
One last thing to think about - who said API is only a REST API, you can add views on top of the data that belongs to another service and as long as you treat that like an API (security, versioning etc.) you can have other services access that as well