A .soe file is simply a ZIP file containing the following items :
- Config.xml
- Install (directory containing : )
- *.dll
- *.pdb
If the Config.xml file is generated (and your dlls) then you can pack it yourself and upload it on ArcGIS Server.
I found that there is a similar issue reported in our system as [#NIM093779 Problems with .NET SDK SOE templates at 10.2 in Visual Studio 2012 prevent the .soe file from being generated. ]
The cause of this bug and the issue you are having are the same.
The workaround would be :
Edit the project file *.csproj:
Near the bottom of the XML you will see an Import element. For both Project and Condition, update the path from Server.targets to Server.11.targets.
Just followed the steps in the workaround from #NIM093779 and it worked, didn't have to do anything else.