Using Windows Embedded Compact 2013 (WEC2013) it's impossible to develop a Net CF 3.9 application without an SDK.
There isn't a default SDK. In general, when you have an embedded system, it isn't general purpose but it has specific features that the OEM exposes with a custom SDK. In this way, avoiding standard SDK, who develop application can't use feature that there won't be on the target hardware.
The only way you have to start develop is to install Platform Builder and using built in CEPC BSP to create a CEPC image for a virtual machine and an SDK for it. After installing this SDK you can use your virtual machine with CEPC image to run your application. In this way you can create an "emulator" for a x86 system with WEC2013 on it.
Paolo.