Something similar was taking place in drupal 7.

I have hook_views_query_alter in file in the same folder as module file. I found out, that query handler is class views_plugin_query_default. Within that class:

  function alter(&$view) {//dpm($view);
    foreach (module_implements('views_query_alter') as $module) {//dpm($module);
      $function = $module . '_views_query_alter';
      $function($view, $this);

Is called, but can't find any module that implements hook...

Of course I cleared all the caches, even truncated tables cache_views and cache_views_data, all in vain.

AFAIR in drupal 7 similar problem solved itself automagically after some time, and hook_views_query_alter started to work. So maybe there is something else cached somewhere? Maybe .inc file is not being seen by backdrop? Access rights are as usual...