I've been lucky enough to work in an Institute that views its core facilities as a cornerstone of the scientific output, and we get acknowledged for most of the work we do. Other core facilities are not so lucky; and even here sometimes people simply forget to acknowledge everyone they should have in the rush to get their paper submitted.
Now the journal BioTechniques has introduced a new editorial policy that will require authors to answer the question "if they worked with a core laboratory", and if so make sure this is acknowledged in the final manuscript. I hope other journals will take a similar decision. All core labs are funded, completely, or in some part, by grant income and are effectively subsidised. This is the main reason core labs are usually cheaper than commercial providers. This funding is not wasted by the host institution as the cores (should) offer a more flexible and bespoke service.