The relational algebra permits interchangeability of the predicates in the WHERE clause and the INNER JOIN, therefore even INNER JOIN queries with WHERE clauses will have the predicates rearrranged by the optimizer so that they will be already excluded during the JOIN process.
In some cases that includes making the INNER JOIN relatively "incomplete" and putting some of the condition in the WHERE clause just to make the lists of filtering conditions more easily managable.
As for example, instead of using the below code:
SELECT *
FROM Customers c
INNER JOIN CustomerAccounts ca
ON ca.CustomerID = c.CustomerID
AND c.State = 'NY'
INNER JOIN Accounts a
ON ca.AccountID = a.AccountID
AND a.Status = 1
Use this code:
SELECT *
FROM Customers c
INNER JOIN CustomerAccounts ca
ON ca.CustomerID = c.CustomerID
INNER JOIN Accounts a
ON ca.AccountID = a.AccountID
WHERE c.State = 'NY'
AND a.Status = 1