Something you can try assuming the area is not obscured by wood or paint.
Take a 3 x 5 piece of paper, cut a dime size hole in it. Hold the paper on the transom area and slowly scan around.
If the HIN is there you'll see it.

Welcome Aboard, Alex.  The stamping is probably there but you'll need a magnifying glass.  
Can you post a picture of the exterior transom ?  Any pics of the Vag will narrow the year down.

















 

Hi Alex,  Your Vagabond was made well before HINs were implemented in 1972. Unless the transom was cut down or replaced your serial number should be there in this format . The stamping is crude and typically much smaller that you'd expect. It also might be obscured by paint or larger than original wood parts attached to the transom.
If it really has been removed your only recourse, if CA won't issue you one (as some States will), is to just make up a serial, following the original format, and apply it yourself.

Greetings - I have a Vagabond I purchased last year from a (Picker) like the American Pickers on TV, that doesn't have the stamped VIN on the transom. How do I go about registering my Feather Craft with my DMV? I live in California. Any experience out there will help!

Than you... Alex