Let's walk through this...return is completed including entering total allowable medical expenses on Sched A line 1. Doesn't matter if the client will be able to itemize - just need that amount entered to determine what medical expenses exceed the 7.5% of AGI which will be on Sched A line 4.   You will use the amount on line 4 for the Form 5329 amount to be excluded from 10% penalty.       Done.

If line 4 is zero then the client doesn't have any medical expenses that will reduce F5329 penalty.  This is completely possible even if your client had a large amount medical expenses but also has a very high AGI.     . 

None of the above has anything to do with the client itemizing or using standard deduction.  You are simply using Sched A Line 1-4 to do the math for the amount of medical expenses that exceeds the 7.5% AGI.   Or you can do the math without using Sched A but why not let the computer do the math for.