Does the comparison respect the current language and shop, and what happens to disabled products?

Yes. When the comparison page requests product data, the module loads each product using the current shop and language from the PrestaShop context, so names, short descriptions, prices and features are shown for the store and language the visitor is browsing.

Products that are disabled, or that can no longer be loaded, are skipped automatically and simply do not appear in the table, even when their ID is still saved in the browser. Comparison is done at the product level, so the table does not build a separate column for each combination of a product.