as far as i got, stock reconciliation is used either for stock opening and to upload physical stock counting for a warehouse at the end of the year.
What happens to all Items not present at the physical counting time? All of that should be considered ad 0, any hint on the easy way to manage that kind of situation?
If items are not present at the time of physical counting, you can create a Stock reconciliation entry with 0 quantity. If you are making Stock Reconciliation for correcting stock level or valuation of an item, then you can select any expense account in which you would want difference amount (derived from difference of valuation of item) should be booked.
Please refer the link to learn more on Stock Reconciliation. https://frappe.github.io/erpnext/user/manual/en/setting-up/stock-reconciliation-for-non-serialized-item