The Id column in your subquery is the Id of the PricebookEntry object. You want the reference field to Product2, Product2Id:

SELECT Id, ProductCode 
FROM Product2 
WHERE Id NOT IN (SELECT Product2Id 
                 FROM PricebookEntry 
                 WHERE Pricebook2 = '01si0000003vpAlAAI') 

The Id column in your subquery is the Id of the PricebookEntry object. You want the reference field to Product2, Product2Id:

SELECT Id, ProductCode 
FROM Product2 
WHERE Id NOT IN (SELECT Product2Id 
                 FROM PricebookEntry 
                 WHERE Pricebook2Id = '01si0000003vpAlAAI') 

My first stop with this kind of issue is always the field reference for PricebookEntry (or whichever sObject is in question). It's a great resource for not just names but specific requirements and limitations around each standard field.