If I delete users from SP (AD), how will that affect metadata (e.g. created/modified by in file metadata, or person lookup fields). Will I end up with anonymous ugly SIDs?
You will not end up with anonymous ugly SIDs. Actually created/modified by fields are not tied to the user profile directly, but to User Information List which is storde in UserInfo table in content database. Even after a User Profile is deleted, entries in UserInfo table is not deleted though a time job runs in every few minutes to sync them. Because of UserInfo table you can view user name in create by/modified by field. But please keep in mind actual user profile gets deleted once you delete one user profile from AD, so you should not expect them to come in people picker search.