Some of it is not due so much to negligence as to bad e-book file prep and buggy conversion tools.
KindleGen will omit your TOC from both the "Go to" function and the flickable chapter marks if you don't specify the files exactly right in the OPF when assembling the Mobi.
But yeah, a lot of publishers seem to be pretty lazy and cut corners when it comes to producing e-book editions, for which they then charge nearly as much as for the paper version.
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