It can be numerous things – filters, incorrectly set limits, exclusions etc..
The result limits can be set here, but I highly doubt it’s the case. Nevertheless make sure it is set to a high number according to your needs.
It is also possible, that some items are excluded from search. WooCommerce will automatically remove those items from the results page in most cases – but they are still counted on the back-end when listing by category. This is the most likely scenario.
Also check if there are no category based exclusions set here. This also happens very often.