Yes, it happens on startup of a fresh Claude Code / Codex CLI session. They effectively get pasted into the system prompt.
Reading a few dozen files takes on the order of a few ms. They add enough tokens per skill to fit the metadata description, so probably less than 100 for each skill.
1) After deciding to use a skill, open its `SKILL.md`. Read only enough to follow the workflow.
So you could have a skill file that's thousands of lines long but if the first part of the file provides an outline Codex may stop reading at that point. Maybe you could have a skill that says "see migrations section further down if you need to alter the database table schema" or similar.
Knowing Codex, I wonder if it might just search for text in the skill file and read around matches, instead of always reading a bit from the top first.
Reading a few dozen files takes on the order of a few ms. They add enough tokens per skill to fit the metadata description, so probably less than 100 for each skill.