Beacon beam goes through certain blocks

Those blocks are "transparent" for the game

Light and the beam can pass through these 'transparent' blocks.
This is normal.

Yes, but the piston? The chest?

Yes, the game considers them transparent.

Every block which is not 1x1x1 blocks large is "transparent", read on here http://www.minecraftwiki.net/wiki/Opacity

(Note that extended pistons are not full blocks, and retracted ones are technically the same block.)