[SalesForce] How to check if a text field is not null, not empty, doesn’t contain white space in SOQL

I cannot seem to reproduce what you've described, I get the sObject not retrieved error for Case 1 too!

The only caveat would be that since sObjects are passed by reference, hopefully there isn't a sneaky bit of assignment which is setting the value of CustomField1 somewhere in the foodchain.

If there is an assignment of value then it wouldn't throw the exception for any subsequent access. (Even though it wasn't initially retrieved as part of the soql)

As a simplified example, this will throw the SObjectException (assuming you have at least one Opportunity):

Opportunity opp = [select Id, StageName From Opportunity limit 1];
System.debug(opp.Probability);

And this will not (opp.Probablity will be null):

Opportunity opp = [select Id, StageName From Opportunity limit 1];
opp.StageName = 'foo';
System.debug(opp.Probability);

You instead need to be assigning it directly to the list:

List<User> ccUsers = [SELECT Id FROM User WHERE ContactID = :joint.contact__c AND isActive = true LIMIT 1];

if (ccUsers.isEmpty())
{
  //Do something because we found no matching Users
} else
{
  //Do something else because there is a matching user
}