this has been discussed many times already. there is no particular technical reason to use PNP vs. NPN or the other way around. it's just polarity so it's relative term (in fact there are plenty of devices that can convert signal from PNP to NPN and the other way around).
things do get another meaning when making industrial machinery vs. school project - because of safety. as long as you don't just try to make it work (bring signal into or out of PLC) but also think about uncontrolled motion (or whatever other hazard it may be such as automatic start, failure to stop etc.) you are wellcome to use any. the basic rule is to ensure that any SIGNAL potential is DIFFERENT from ground potential. in NPN system that would be -V, in positive it's +V, but always potential different from ground.
consider first image where NPN output is driving load. notice that emitter of NPN transistor is shown as grounded. imagine that load is something that causes motion (solenoid valve of some actuator or start command of VFD drive etc.). if you have failure such as short to ground BETWEEN the output and load, load will be energized (not by PLC but by that accidental short) which means you will get motion when not expected (and possibly hurt someone). this is classic example of poor design although electrically circuit can operate if everything is ok (problem is when something bad happens - and this is part of good design). it can be corrected by grounding positive end of the power supply instead of negative (this is hard to digest as many people still freak out when some mentions grounding of DC side of the power supply). same goes with inputs where short to ground could cause accidental start etc. or where both inputs and outputs tie to same PSU rail (negative for example). this (both inputs and output devices tie to same potential) is quite common in low power electronics (not enough energy to hurt someone) but this is NOT good enough for industrial shop flor.
as for NPN input LED indicators being on when sensor is not energized - i've never seen this and I'm using both PNP and NPN a lot and variety of platforms. When diagrams of internal circuitry are available, they show that LED is in series with input. Maybe ToolGuyFred can explain which PLC he meant.