How does it shift ? Does it feel like it always shifts late and harsh ?
The vacuum modular is how the transmission senses engine load and knows when to shift (as you may know, can't tell from your post). So with no vacuum signal it would be strictly relying on the governor to shift once it gets to a high enough governor speed. Plus the modulator not being hooked to vacuum will mimic the engine always being at high load.. Usually that will create a late and harsh shift.
There are some "shift improver" kits that could have been installed that would bypass the modulator signal, BUT "to my knowledge" the only ones that bypass it are set to manual shift mode only.
I would hook it up.
1999 American Dream 40DVS
Spartan Chassis, Cummins ISC 330