How to override ID's in Drupal and comply to CSS Lint|?
Using a subtheme you can override whatever templates contain IDs and change them to use classes instead, updating the CSS along the way. 

For example you can override the node template by creating a node.tpl.php file in your subtheme, and the markup can be changed to whatever you need.

You'll have to identify which templates need to be overridden yourself, as there isn't a list available; it will depend on what modules you have installed, and what base theme you're using.

It's also worth bearing in mind that contributed modules (and possibly core modules) may use IDs to target elements in javascript. So test thoroughly, as you might need to make some changes there as well.

However

Don't forget that you're just trying to comply with CSS standards here. You don't need to actually remove the IDs to do that, just any CSS that uses them in selectors.

Drupal 8 core conforms to the rule anyway (see .csslintrc in the root), so you should be covered there, but contributed modules may not. That's when you'll need to check manually and maybe override templates/CSS files that they provide.

Earlier versions of Drupal don't conform to the same standards as far as I know so YMMV.