1. In ArcMap, Right-Click to open Layer Properties form and Click the Display Tab. And set the value for Layer Transparency %.
2. Once you Analyse the map service, make sure to USE COLOR TRANSPARENCY.
3. Once this map service is published, re-load the Server Catalog so that Dekho is able to see it.
4. When creating Template for this map service, change the IMAGE FORMAT to PNG32 to make sure Dekho respects the Transparency.
Now, the Dekho Map created using this template will show transparency as set in the map service.
This is exactly the same process as in the previous version, the only change is that in the previous version you had to use a description tag IMAGEFORMAT=PNG32; in the config mxd and now this is a setting in template.