ATC can only identify aircraft if they have a proper active transponder. Even if the primary radar detects the balloon, if the secondary radar won't get an answer, the balloon won't be identified as aircraft.
Small balloons (under 2kg) are considered as low risk objects, so internationally they won't need any active transponder to answer to secondary ATC radars. Larger balloons must be equipped with C-transponder and operators have to follow a procedure to communicate with ATC (at least in Hungary)
In Hungary we have three balloon categories: Light, Mid-size and Heavy.
Light unmanned balloons don't need either transponder nor radar reflector and you only have to submit a launch plan (where, when, what will you launch). Also as far as I know these balloons are filtered out by the radar algorithm (like birds and such). Light balloons can be launched from practically anywhere, no detailed restrictions for that.
Mid and Heavy unmanned balloons must be equipped with C-transponder, radar reflector and FTU. All flight activities must be reported to the local ATC (like launch, burst/flight termination, landing). Launch site and launch procedure is regulated by law for these balloons too. But there was no precedent for Mid-size or Heavy balloon launch in Hungary so far.
We are launching balloons in the 'Light' category, but we use radar reflector anyway. We are planning to upgrade to 'Mid-size' category later, but we have to clarify the legal background for that (since there was no such balloon flight in Hungary yet)