For habitats, almost all of the population works in manufacturing, ignoring colony cost. That's the main reason to use habitats: colonizing high-cost worlds that infrastructure wouldn't cut it on.
I'm pretty sure a habitat can hold colonists in cryogenic storage for travel. Also, I believe that 10,000 colonists serves the same function as a recreation module, so you shouldn't need one in your habitat.
Edit: Here's a hypothetical design I just drew up:
Terra Nova class Colony Ship 8,256,650 tons 11360 Crew 70435.4 BP TCS 165133 TH 40000 EM 0
242 km/s Armour 1-3638 Shields 0-0 Sensors 1/1/0/0 Damage Control Rating 1 PPV 0
MSP 5 Max Repair 500 MSP
Intended Deployment Time: 3 months Spare Berths 0
Cargo 1250000 Cryogenic Berths 500000 Habitation Capacity 1,000,000
Terraformer: 50 module(s) producing 0.125 atm per annum
Maintenance Modules: 50 module(s) capable of supporting ships of 10000 tons
400 EP Commercial Magneto-plasma Drive (100) Power 400 Fuel Use 4.42% Signature 400 Exp 5%
Fuel Capacity 100,000,000 Litres Range 49.3 billion km (2356 days at full power)
This design is classed as a Commercial Vessel for maintenance purposes
This design is classed as an Orbital Habitat for construction purposes
Contains space for 50 regular-sized installations and 1,000,000 colonists (but only 500,000 in cryogenic storage), has 50 terraformer modules, and can support ships up to 10,000 tons in size. It's also self-propelled, although it's slow.