Can I transfer Kerbonauts from a capsule to Hitchhiker Storage Container without taking an EVA?

Solution 1:

As of the latest version (.18), the ability to transfer crew via docking ports has not been implemented. Fuel can be transferred without a problem, but crew, unfortunately, require EVA to populate the habitation modules.

Solution 2:

It is now possible to transfer crew members without EVA between docked ships.

The KSP wiki has a section explaining how at the bottom of the Crew page:

... in case of transfer option, we can click on an another cabin with free seat in the same craft or a docked together group ...

Not sure which version this was added, but the screenshot on the wiki is dated October 2014.

EDIT:

This was added in v0.25 - see the release notes on the wiki that has a section stating:

Crew Transfer

Kerbals in the same vessel don't need a spacesuit anymore to switch seats. Just click the crew hatch and select Transfer to tell them to go sit somewhere else.

Solution 3:

While there's no stock way to do it as far as 0.20.1, there's a fan-made plugin that implements that functionality and more:

http://forum.kerbalspaceprogram.com/showthread.php/24636-0-20-Kerbal-Crew-Manifest-v0-5-3-0-Released!-Create-Edit-Remove-Kerbals

It also lets you pre-populate the Hitchhiker pods when you launch them, if you so desire.

Edit: still true as of 0.24