Like that Missile Silo in the original SiN.

How many secret levels are there in both SiN and WoS anyway?

SiN has a number of areas where you are able to visit or skip extra maps (like one part where you enter a whirlpool) that depend on what actions you take, whether you complete certain objectives or fail them. I don't know if any of those are properly secret or not. Wages of SiN has no secret levels really, and it's much more linear except for one scene where you make a choice and it affects the order of levels you visit for one part, and whether you play those levels during the day or night.

http://www.gamefaqs.com/pc/39787-sin/faqs/15778
This FAQ has a comprehensive guide to visiting all 36 levels in a single playthrough and finding all secrets.

By secret level I mean levels you can miss out on and cannot go back on it again. Like the Missile Silo, which is the only one I know about.

1. In Freeport Sewers Part 1, falling into the whirlpool will take you to Freeport Aqueducts
2. In Freeport Waterworks Part 2 if you don't turn off all the valves in time, you get to explore the rest of the Freeport City Dam map (not quite the same thing as a secret level)
3. In Hidden Docks Part 1 there is an elevator that will take you to Geothermal Plant Part 1
4. In Geothermal Plant Part 1 there is an airduct that will take you to Geothermal Plant Part 2
5. In Jungle Pass Part 1 there is a stream you can follow that takes you to Jungle Pass Part 2
6. In Containment Area 57, if you destroyed the water pumps in Geothermal Plant Part 2 you can find a passage to Biomass Reclamation Center
The FAQ I listed has a more comprehensive guide to getting to all these optional areas.

Wages of SiN just has the branching set of missions. Choosing one set means missing out on the other. The maps are mostly the same, and that part of the story plays out differently. After that set, both paths return to the same linear path:
http://www.ritualistic.com/games.php/sin/woslevels.php