I work for several beamlines at the Advanced Photon Source. There are probably far, far over 1,000,000 electronic signals at the whole APS facility that use 5 volt signaling. So almost any level shifting will be to embed 3.3 volt signals in a 5 volt world. It is simpler to buy equipment that has already done this.
No doubt. But lots of Arduinos have been used in scientific experiments because they are inexpensive and easy to work with. So the choices made in Arduino-like boards do affect us.