Generally speaking,
upgrading to a slip-on affects sound rather than performance and upgrading other parts of the exhaust that are ahead of the silencer affects performance rather than sound.
That said, reducing weight also improves performance and the Ninja 400's stock silencer is bulky and heavy, so installing a slip-on is a
weight-reducing modification. Installing a full system will reduce weight even more.
The reason a slip-on doesn't improve performance very much is because the silencer is positioned beyond the portion of the exhaust system where restriction and/or exhaust flow has the most potential for improvement.
Upgrading to a full system will potentially reduce restriction and improve flow (these are not the same thing), particularly in the "midpipe" portion of the exhaust. A full system will usually eliminate the catalytic converter, which may or may not be legally permissible where you live.
@
Watcher905 is correct about an ECU piggyback device or a reflash being required to achieve full performance.
Consider also that you want to avoid a lean condition. Bikes tend to run lean from the factory, and de-restricting the exhaust and/or the intake can lean things out even more. For some bikes the lean condition is a critical concern and for others it's less of a concern. I'm not qualified to say how important this is for the Ninja 400, but others on the forum probably are.
IMHO a slip-on is a compelling mod because it improves sound, reduces weight, and looks good. A full system is less compelling because the Ninja 400 stock exhaust seems to be better than most, and replacing it contributes to a lean condition and I'd prefer to avoid that.
I'm lurking around waiting for some feedback from
BoosterPlug pioneers.
Removing the airbox snorkels is another mod to consider.
Also related:
PAIR valve removal