As their name belies, SDB's are just that - System Defense Boats. In systems where they are deployed, they tend to stooge around (i.e. lurk) on the fringes of the system, or hiding in/near gas giants. Their job is to harass/destroy the enemy. At 400 tons, and while they are heavily armored, they are annoyances to larger warships, but potentially deadly to lightly or unarmed enemy transports, tankers and other support craft. A 5,000 ton destroyer could easily take on and eliminate a handful of SDB's. But a 10,000 freighter or tanker (assuming they aren't heavily armed) could take significant damage from the SDB before help arrived - if not being outright destroyed.
So their effectiveness would be greatly reduced if they were out in the open most of the time. You wouldn't normally encounter one near inhabited planets or in primary shipping lanes because they would shun being exposed. Think of them like attack submarines of today. Subs don't pop up to say 'hi!' to surface ships. Their job is lurk in the depths, to be hidden while they play cat-and-mouse with their prey.