I've heard about this from librarians, and they always emphasize that they don't want to discourage people from checking out eBooks because of this! Showing support for the library is important, even if it is a bit more costly. It probably also depends on library size, though. We have a huge county library system, so there's usually "1 bazillion copies of Best Seller, provided by Donor!" on the front page of the ebook library site.
For more niche titles, it might make more sense to request as a physical book rather than an eBook for the reasons you stated (physical copy will last until the next eclectic person wants to check it out). That or buying the occasional physical copy yourself and donating it when you're done. We've done that with niche things that we don't expect the library ever to really have enough of a reason to purchase.