We did not change the page size, instead we only set a higher values to the Cache size in the connection string as shown below:

@"data Only=False;FailIfMissing=True;cache_size=-100000"

And this fixed the issue. The queries run without any slowdown in the encrypted db.

However, we still dont have the actual reason why the issue occured in the encrypted database only. Also, will there be any sideeffets with the fix we made?