It sounds like you're pretty certain the algae is clogging the drain pipes. IMO, You either need to change the plumbing and/or overflow or correct your algae issue.
Changing the overflow could/should be more than "putting a box around it". Popular styles like the bean animal have multiple return lines. If one clogs, you hear the emergency splashing, hopefully in time to fix the clog. Obviously if the algae is bad enough to clog the emergency within the time period between which you look at your tank (a really bad algae issue) it could still fail but that seems rather extreme.
You could change your return pipe diameter to make it more difficult to clog.
You could simply change the return bulkhead screen with a larger one that either lets the algae through (to be caught by mechanical filtration like filter floss or a sock) or one with a larger surface area so it takes longer to clog.
Ultimately, as it seems there's the inevitable, "but eventually all those will clog" response, it sounds like you gotta correct the algae root cause and keep a close eye on it until you do.
I would add that this may be a time to consider a different overflow setup as I'm not sure this is common for people who have overflow boxes. The weirs have a long set of perforations to clog and the actual plumbing has no screen to clog.
Good luck!
