As far as I recall, Alerts are amazing. They strip user rights, and make everyone else able to see the user(in addition to the +4 firewall bonus for restricted alerts). yes, they are rather bad, and you should strive not to trigger them.
1) You don't have any rights, and have to rely in Hacking to do anything
2) everyone can see you
3) the system is calling for backup.
There's also this from the FAQ, for what its worth.
QUOTE
Q:When you trigger an alert, will security automatically spot you, or do IC and security hackers still need to succeed in an Opposed Matrix Perception Test?
A: IC or security hackers will need to spot the intruder as normal, unless a Restricted Alert was issued. If a Restricted Alert has been issued against the Hacker, IC and Spiders (users with a legitimate account) do not need to make a Matrix Perception Test in order to know of the presence of the intruding Hacker because the Node has already identified them. These icons may attack the hacker or take other actions that target the intruder. They do not, however, know any further information about the intruder beyond the fact of their presence. If defending icons want to know more information (access ID, what programs are running) they must succeed in a standard Matrix Perception Test.