Those thank-you notes matter, even if fundamentally the reason for giving is completely based on the actual work.
I think it's entirely unsurprising that people would like a thank you email. If you donate to an open source project, you have gone out of your way to acknowledge the project's maintainer. The least they can do is acknowledge you back - it's basic reciprocity.
>the cost of configuring a bot to send thank you emails is so low
Honestly, I think a bot saying "thank you" is as soulless as no "thank you" at all. It doesn't take long to type up a manual response and genuinely express your gratefulness.
I'd be perfectly happy to get a bot reply saying thanks. The main issue I had with silence is when I'm not sure if the money actually got to the maintainer.
I'm less worried about getting personalised 'thank you' as it is easy to see if the developer is still making active contributions.