Yes. The stocktake is based on the stock in the warehouse, not on whether a product is active in your shop. An inactive product that has stock in the selected warehouse or has a default bin location there therefore appears in the Uncounted tab and is booked like any other product when you finish the stocktake.
Why this matters
When you count a bin location, Pickware includes all products with stock on that bin location in the count, including inactive ones. If you did not count an inactive product because you assumed it was not part of the stocktake, Pickware books its stock to 0 when you finish. With many discontinued items, large stock differences can quickly arise, see What happens to products that I do not count on a bin location?
Hide inactive products
In the Uncounted and Counted tabs, you can enable Hide inactive products in the filter menu. This makes the list easier to read, but it does not exclude the products from the stocktake.
Attention: If you save a bin location count while inactive products are hidden, they are still included with 0 and are booked to stock 0 when you finish.
How to proceed
Before you start the stocktake, decide what should happen to the stock of inactive products. If they are still in the warehouse, count them as usual. If they are no longer there, a stock of 0 is correct and you do not need to do anything.
If inactive products are on bin locations that you do not want to count at all, simply leave those bin locations out. Their stock then remains unchanged. If you want to clean up the stock of inactive products beforehand, you can do this with a CSV import in the stock overview, see How do I overwrite my stock via CSV? Do this before you start the stocktake, not in the middle of it.
You can find the complete process in Performing a stocktake: process from start to finish.