Regular iOS App Store apps can exchange files with computers via iTunes by turning on UIFileSharingEnabled in their Info.plist. The files exchanged are placed in and/or retrieved from the Documents directory for the app. Jailbreak/Cydia apps, being System apps, don't have such a directory--so I'm assuming they can't use this feature to exchange files with a computer? (Obviously jailbreak devices have more options to exchange files like ssh.)
EDIT: Just to be clear, I'm talking about system apps, not regular apps that happen to be headed for Cydia for whatever reason.
Yes. Cydia apps can be built using all the features as a normal app IF you are using X-Code