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I'm asking about the relation of WP .php files (themes etc.) with the database. Is (part of) the content of these files stored in any way on the database?

Context: I'm trying to migrate from http to https. All the relevant guides, talk exclusively about a "Search and Replace" of the http://domain with the https://domain in the database. Nowhere did I find anyone mention that you should also do a search and replace in the theme or other .php files of WP; though often there are links/references to the domain in these files.

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No, a theme's .php files are not stored in the database. Themes should not be hardcoding URLs in their files. However, it's totally possible for this to happen, particularly with a custom theme or plugins whose developer did not follow best practices.

I'd suggest using a search utility such as grep (grepwin is nice for Windows) to look within your files just to be sure if your domain appears or not.

Also, when doing a search and replace on the DB, remember to use a utility that is able to handle serialized arrays, since a simple string replacement will damage data. WP CLI's search-replace is one option. WP DB Migrate is really nice too.

Be sure to make a backup of everything before you make changes.

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