This has come up before in some of our conversion jobs. Strikethrough is not accessible, unfortunately. You can style it using the <s> tag or CSS, but the stricken-out text is still read by screen readers (I’ve confirmed after testing an example using NVDA). It doesn’t indicate to the reader that the text is stricken-out.
There’s not much that can be done to remedy this, currently. One way is to capture stricken-out text as an image (if there is a block of text that is struck out) and indicate as such in the alt-text. However, this can be quite convoluted and disrupt the user’s reading experience if there are several instances of struck out text in the book.
You can also indicate in the Accessibility Summary in the OPF to inform the reader that the book contains some stricken-out text. It’s not a complete solution, but it gives the reader a heads up, at least.