I tried to take a list of users with reputation greater than 5 using a Stack Exchange explorer simple query:
select id
from users
where reputation > 5
I get only 50,000 rows. I expected to get millions. Is there any threshold? Is there any way to get them all?
This is a cross-site duplicate of "Why can't I pull in all the SO users from Data Explorer?" on Meta Stack Exchange.
The Data Explorer (SEDE) limits to 50K rows.
Either refine your query or download and use the Data Dump instead. That's what the Data Dump is for.
Alternatively, you can access the Data Dump via Google's BigQuery -- which also has an API.