What is the best way to store files metadata in DB?
What is approx. size of the data? Your no. of rows being a concern here
How often does this data get updated? Consider data access and ACID transactions computation costs in your architecture.
Files metadata will have directories and subdirectories - which are dynamic in nature. Hence schematic representation(RDBMS table) may not be suitable. My initial impression says NoSQL may be a better candidate.
Choose the NoSQL database that suits best - Document DB, Key-Value pair, or Graph database if the files are interlinked (refer to each other) and you need to retrieve that relation
If you need to use RDBMS unless it is too old, many of them offer JSON capabilities inbuilt, please consider the same.