Yes, the early 400s had 3 on each side.400 small block blocks have 3 freeze plugs on each side of the block. The smaller displacement blocks do not have this (only 2 per side).
Later blocks had two plugs, with a non-machined boss for the center plug. The latest blocks had the usual two core plugs with no center boss just like the other small-blocks.
"In general" and with exceptions, the 3-core-plug blocks also had 4-bolt mains. But things were kinda goofy with the 400s, I've seen a block that was drilled but not tapped for the outer bolts, and had 2-bolt main caps.