I ended up doing the following test, to exclude rqlite from the equation:
1) started rqlite in disk mode and created the data base
2) made a simple c# client to connect to the data base and execute parallel queries
3) the problem is the same: 2 queries in simultaneous (creating a new connection for each read), almost doubles the response time comparing to a single query.
So this as something to do with sqlite, I suppose.
Regarding rqlite options I'm not setting any read-consistency level and i'm using only one node.
The query is a bit complex. But I will try to provide a testing sample.