Occupancy rates Appendix 2 Daily averages or peak occupancy

Appendix 2 typically applies to Core/Shell projects, only occasionally new construction. There is a section of text in the Getting Started section of the BD+C guide that explains when projects can use App 2:

"Buildings and spaces that earn LEED certification should be completed by the time they have submitted their final application for LEED certification. Complete means that no further work is needed and the project is ready for occupancy. No more than 40% of the certifying gross floor area of a LEED project may consist of incomplete space unless the project is using the LEED BD+C: Core and Shell rating system. Additionally, projects that include incomplete spaces must use Appendix 2 Default Occupancy Counts to establish occupant counts for incomplete
spaces.
For incomplete spaces in projects using a rating system other than LEED BD+C: Core and Shell, the project team must provide supplemental documentation.

• Submit a letter of commitment, signed by the owner, indicating that the remaining incomplete spaces will satisfy the requirements of each prerequisite and credit achieved by this project if and when completed by the owner. This letter may cover the commitment in general terms and need not address each prerequisite or credit individually.
• For incomplete spaces intended to be finished by tenants (i.e., parties other than the owner), submit a set of nonbinding tenant design and construction guidelines, with a brief explanation of the project circumstances. For prerequisites with established baselines (e.g., WE Prerequisite Indoor Water Use, EA Prerequisite Minimum Energy Performance) and the credits dependent on the calculations in the prerequisites, the proposed design must be equivalent to the baseline for the incomplete spaces. Project teams that wish to claim environmental performance or benefit beyond the baseline for incomplete spaces should refer to the Tenant Lease and Sales Agreement section."

So, be aware of the additional documentation needed if you do, indeed, fall under the 40% threshold and still need to use App 2.

That said, the values there represent average occupancies, not peak. If peak is needed for some calcs, you'll need to determine how to arrive at those values for your project, and likely supply a narrative with your documentation explaining your assumptions. For a mall, it would probably be expected to have the peaks around holidays.

It's meant to be an average for any given day (not a moment in time), so I guess it does represent an accumulated total per day. 

The hours of operation should not play into this calculation; the transients are assumed in a 24-hour period.

Also note these statements in the Getting Started text:

• "In Water Efficiency credits, retail customers are considered separately from other kinds of visitors and should not be included in the total average daily visitors."
• Found this one, too: "If numbers vary seasonally, use occupancy numbers that are a representative daily average over the entire operating season of the building."

The online version of the front of the Ref Guide can be found here: https://www.usgbc.org/guide/bdc 

When I've had a complex or atypical project in the past, I email LEED Coach directly with my assumed occupancy values and get their blessing before moveing forward with the design or calcs.

The Appendix 2 values are definitely averages, not peak. Are you seeing a specific credit in the Core/Shell version that is asking for a peak calculation? The indoor water use prereq/credit does not use peak values.