Why are they similar?
Externally, reapers follow a set design (though the armada seen at the end of ME2 shows that there is room for some variation), but internally capital ships contain a core which is roughly in the image of the one species which is harvested to create capital ships.
What are destroyers made of?
Whilst it is not definitely specified (as far as I can find) whether destroyers contain such a core (it could be inferred from  but that may just refer to the capital ships), the codex says that they are created from all the other species which are sufficiently advanced to be harvested (Remember that not all species are culled in the cycle - Javik references this many times in ME3) but not the chosen 'capital' race.
Codex: The Reapers - http://masseffect.wikia.com/wiki/Codex/The_Reapers#Reaper_Variants
CAPITAL SHIPS are Sovereign-class Reapers two kilometers in length. They typically target the dreadnoughts, defense installations, and industrial cities of organic civilizations. Experts believe the Reapers harvest a single species of organics during each cycle of extinction to create these massive ships. Some capital ships are capable of launching small drones equivalent to fighters.
Interview with writer, Mac Walters - http://www.gameinformer.com/b/news/archive/2011/04/21/mass-effect-a-q-amp-a-for-hardcore-fans.aspx
The exterior of the Reapers does follow a similar pattern, an efficient design for the purpose they were created for. However each Reaper is created from a unique species, and as we saw at the end of Mass Effect 2, the core of each Reaper is designed in the likeness of that species.
Codex: The Reapers - Same link as 
DESTROYERS are 160 meters long and, in astounding numbers, make up the bulk of the Reaper fleet. They engage cruisers and other, smaller ships, as well as communications posts and enemy command centers. Research suggests destroyers are created from those species that are not harvested to make capital ships.