1000 tables isn't an extraordinary amount. As far as database schema design goes it really depends on your needs, e.g. is your database intended for OLTP or OLAP use? Depending on your needs you can decide to what degree you want to normalise your tables, also there a lots schema designs to chose from (star, snowflake, etc.) and it's worth reading about them. Having a good schema design is about knowing the data you have and how you plan on using it, there is no one "good" solution in my opinion.
Edit: Security is also something worth taking into account, design for the applications and users that are going to access your database. You might create a separate schema for an application and separate schema for users and then grant them access to a "main" schema for instance, but this really all depends on your needs in the end.
Not a database person but 1000 tables does seem like an extraordinary amount imo. At that scale I wonder if such a use case warrants a document based database...
I have been working in the banking industry since 2015 as an Oracle database developer and contractor and having a few hundred or several thousand tables in a single database schema is typical. In a single ETL or ELT process you can have several different tables such as staging tables, configuration tables, tables for slowly changing dimensions, enrichment tables, configuration tables, temporary tables, tables for exchange partition, etc.
On a somewhat related note: the OpenType (OT) font format specifies 55 different "tables". These are not really what would be a table in a database but more like sections that may have multiple tables. E.g. the "math" OT table has constants, glyph info, italic corrections, top accent attachment, kern info, variants, glyph construction... -- I can't say for sure but I think a hundred tables to properly describe a font is probably a good estimate.
Edit: Security is also something worth taking into account, design for the applications and users that are going to access your database. You might create a separate schema for an application and separate schema for users and then grant them access to a "main" schema for instance, but this really all depends on your needs in the end.