I would normally ALWAYS put some sort of circuit protection on inputs. For the main reason that if there is a short on one of the input wires, you can easily figure out which wire is the offending wire. Field shorts certainly occur more often than we'd like, IMHO. Having an entire machine fail when there is one short - and having to try and figure out where the short is amongst maybe a hundred inputs - is really ugly.
At a minimum, you need circuit protection on your inputs to ensure the power supply doesn't crowbar from a field short or an unsafe condition doesn't occur from a field short. This safety discussion is assuming you are using sourcing inputs: sinking inputs only have ground potential so safety is not as big a concern. But I rarely use sinking inputs: too confusing for most troubleshooters.
So with troubleshooting being the main reason to fuse groups of inputs, it is common to gang a few inputs together on one fuse (maybe 8 on the same fuse). Then if there is a short, you can at least narrow it down to a group of 8 wires with the short - then start chasing them down one at a time.
Another alternative to fuses in a DC system is to use PTC 'fuses' that heal themselves once the short is removed. Very convenient for the operators: fix the problem and there is no fuse to replace. With the PTC, it is also possible to build a little companion circuit that lights an LED if a short is detected and therefore makes it real easy for the operators to figure out which bank of eight inputs is having the problem. If I recall, Weidmuller sells some pretty nifty circuit boards that make it easy to circuit protect your inputs in groups.