What method(s) would law enforcement / spy agencies use to get intelligence or information or evidence if they were not allowed to spy on every citizen by listening in on calls and reading emails?
Some very high level people in several law enforcement / spy agencies have already said that it is impossible to catch anyone if information against everybody is collected, because they would be swamped with so much information that filtering out anything useful is completely impossible. So it's quite the opposite of your question.
And what methods would they used if they were not allowed to illegally spy on everyone? Whatever is legal, just as they do now. Undercover work, appealing to concerned citizens who have information. Education to destroy the basis of terrorism. Being intelligent. You don't stop terrorism by catching terrorists. You stop terrorism by stopping people from wanting to be terrorists.
In fact, they are currently not allowed to spy on every citizen by listening in on calls and reading emails. The federal wiretapping law 18 USC 2511 limits that power. This is not to say that the existing broad power is justified, so one might revise that law to make it more difficult for agencies to engage in wiretapping. You could simply massively simplify the law and make all interceptions subject to two-party consent.
Supposing that you did this, it would still be legal to use information reported by individuals; you could still take note of the comings and goings of individuals coming into the country. There are very many law-enforcement tools that are used to catch criminals and terrorists, and it doesn't just rely on wiretapping.