Performance implications of adding a "disabled" column to a table

Greetings,
I have a large number of rows (up to 3-4 millions) that I'll either be fetching into ram (if it is a few thousand rows), or scrolling through a cursor.
Deletions or updates on content of these rows lead to expensive operations in my business logic, so I simply need to mark them as disabled.
I have two options here: to exclude the disabled rows from my query results via ..where not disabled or to not to process disabled rows in business logic.
There will be very few disabled rows compared to total rows I'll have to return. This table will have very few queries, so including disabled = false or enabled = true in every query would not be an issue

I have a feeling that including this criteria in the queries may add  unnecessary processing to my queries, since the table is expected to get up to 100 million or more rows. So should I deal with this in DB, or at the application layer?

Kind regards
Seref