It just takes one system shutdown again to cause 1000's of PAX not being able to check in.
frfly - not quite sure I follow your reasoning here.
The important thing is to ensure that passengers can checkin online over as wide a time window before departure as possible. As Ryanair do not sell flexible tickets relatively few people have a need to delay webcheckin until only a few hours before departure.
If webcheck is open online from (for example) 5 days in advance, this leaves plenty of time for people to print the boarding pass at home. If one tries to checkin 24 hours in advance and the webserver is down.... just wait a couple of hours and try again. FR would be wise to strongly encourage pax to checkin early rather than leaving it to the last minute. Many major corporate websites are outsourced to 3rd parties with 24/7 monitoring and reliability guarantees - the sysadmin team should have specific instructions as to how to restart the webservice for each of its clients in the event of failure. I will assume that Ryanair are taking a similiar approach.
Once initial teething issues are resolved, IT systems like webservers tend to experience failure when they are put under a high degree of strain - either an unexpected surge in people visiting the website or because earlier warning signs of IT server strain were repeatedly ignored. Sometimes I have difficulty booking a flight at 8 pm in the evening - I've never had a problem at 3 am.
5 years ago, when everyone had to checkin at the airport, there would have been a big surge in boarding card issuance around 6 am on Saturday (and thus a higher risk of major system outage at a really bad time), but Tuesday mid-afternoon would have been relatively quiet. By moving to online checkin and spreading the demand for checkin over the week, the 6 am spike is reduced, and the webserver is less likely to experience a major outage.