Nailgun is not a good solution to the problem. If the JVM startup speed is a problem, your best option is to use something not on the JVM and not use hacks that make it feel faster.
That's not true. Yes, it's worth considering outside of the JVM if being on the JVM means your application isn't interactive enough (startup speed doesn't matter for long running, fire & forget tasks).
At the same time, splitting your application into a client/server architecture is not a hack but an engineering decision. There are times when this decision is natural e.g. Music Player Daemon (MPD)[1]. For most CLI applications, there's no clear benefit (but the general approach has no clear downside either - the code overhead of this approach can be brought very low).
Certainly, in a production application you would want to secure the messaging channel (Nailgun doesn't).
At the same time, splitting your application into a client/server architecture is not a hack but an engineering decision. There are times when this decision is natural e.g. Music Player Daemon (MPD)[1]. For most CLI applications, there's no clear benefit (but the general approach has no clear downside either - the code overhead of this approach can be brought very low).
Certainly, in a production application you would want to secure the messaging channel (Nailgun doesn't).
[1] A music playing server: http://www.musicpd.org/. Some of the clients happen to be command line: http://mpd.wikia.com/wiki/Clients#Command_Line_Clients