All these messages have to take turns. It's not a tracker, or a modular synth, where you can parallel click rise times electronically: it's not DINsync, where a chain of voltage pulses synchronize individual sequencers and aren't themselves notes.
1000 messages a second (at three bytes for each note-on) seems like a lot but it really isn't. With your 16 instruments (any drum, the xylophones, whatever) you can fire about 62 notes on all instruments per second. That seems like a lot too, but it's a hard limit, and it means your sixteen instruments have to 'blur' across 16 milliseconds to all fire off a note.
That means every time you fire all the instruments as one click, instead the attacks make up a 960hz tone. That's NOT one attack. Humans on percussion instruments can do better than that. It's the equivalent of 5.5 feet of space between speakers playing back: if you're time-aligning a tweeter and a midrange to produce a unified click, and you misalign one of the drivers by putting it five and a half feet back from where it would be, you'll notice the misalignment. Midi's timing issues are also noticeable.
Consider that Hollywood composers and music producers are able to use MIDI without issue for live-previews of orchestral compositions and live recordings and performances. The problem you are raising simply doesn't exist in the real world, accept that there are things about MIDI you don't understand and move on.
Still ain't quite DINsync or modular, but there ya go :)
However, if you want to control attack, reverb, tone, volume, i.e., all the stuff that makes it seem like a real instrument and not a computer-generated tone, then you would need to dedicate some of the 16 channels on each port to each of those different controls. To handle 16 xylophones, you would need a MIDI interface with enough ports to handle the note data plus however many control channels you want to use. (Note that from the interface's perspective, the data incoming from 1 port is just a single channel, so an "8-channel" MIDI interface is actually handling 128 channels of MIDI data.)