Metadata creation is generally one time activity and as you have mentioned because of many tables present in database, you are struggling with creation of metadata. In this kind of scenario we recommend 2 solutions:
Create a database user on your database server itself which is having access of only limited tables which are actually required for creating a metadata/report. Then you need to make your datasource connection in Helical Insight with this DB user having limited and restricted access and not access of all 1000+ tables.
Even if you made connection with db user having full access (1000+ tables) like you have currently done, then at Datasources page of Helical Insight while making the connection (Even you can edit already created connections) restrict the tables, catalogs, schemas exposed at metadata page.
For example in case of table ->On the datasources page, edit your connection and click on Advanced and you will see Other Options placeholder. In this placeholder pass filter like ?HI_TABLE=table1,table2,table3 etc comma seperated table names which you need to create metadata out of this 1000+ tables and save this datasource connection. This will restrict the tables to the number of tables which you have passed in COMMA seperated way.
For more details of this refer this blog :Restrict Tables, Catalog, Schema Exposed At Metadata Via URL