Interesting, because AS's website says you can:
Need to add a Mileage Plan number to an existing reservation? Please visit
elal.com, or call EL AL Israel Airlines at 1-800-223-6700 or Tel. 03-9771111 / *2250.
Presumably you can still contact customer service with a boarding pass after the fact for manual credit, but it's of course more convenient to get it automatically.