The difference (according to the gpg agent log) is that gpg v1 is obviously caching
the decrypted private key used to decrypt the files using the option "-d --
multifile" whereas gpg v2 in my case repeatedly requests the decryption of the
private key for each single file. Any way to change that?

Well, I can only say right now that since upgrading to Ubuntu 16.10, the gpg
command now is gnupg v2 by default, and my parallel decryption using
multiple gpg processes does not work any more. "Not working" means there is
only one gpg-agent processes using any CPU at all, and it is using only one
CPU core at 100% for a very long time. Nothing else pops up in top regarding
CPU usage. 75% of the CPU cores remain idle. So my guess is that the gpg-
agent does all of the work and therefore prevents multiple parallel
executions. My conclusions seem pretty obvious to me. But maybe it has to do
with stuff done by some downstream debian or Ubuntu packagers?