So this is a pretty odd one but for some reason the sound the plays when I reload certain weapons is complete silence, having the issues with the Crysis weapon Pack, Metro weapon pack and Killing Floor weapon pack, it also happenes with one other gun called Pinpoint added from Underground Hideout mod. Everything including firing the gun works but once I reload it, its silent. I installed the mods manually by dropping them into my FNV data folder than merged the .esp's in FNVEdit, got no errors in FNVEdit either. Thanks so much!

Maybe reinstall the mods?

Alright so I've reinstalled as you've said and enabled the .esp's individually and disabled the merge. Still have the same problem but I may have narrowed it down to pistols as the weapons with the issues are the AY69(Crysis), Hammer(Crysis), MK23(KF) and Mac10(KF), they all have the same pistol reloading animation and no sound yet my other pistols in the game work perfectly. Also I should note that I didn't have this problem with the Pinpoint gun before I created a Master update and merged patch, I did try to disable the patch and test out with that gun yet it still had no sounds when reloading, I also did a MasterRestore after that. Thanks btw for replying!  

Oh my god, firstly I would like to apologize to anybody trying to figure this out, It just turns out that I am the biggest idiot ever lol, so when I created my account on here I got really excited and started posting and downloading all sorts of mods and in my mod frenzy I completely forgot to install the OTHER file within Hitmans animation overhaul anniversary called GUN Reloads.esp literally in all caps right below the main file. I'm sorry everyone! But I fixed it by just deciding to check the page and read, if anyone would like to delete this whole topic it's okie!  

So I updated the mod and uninstalled the files of the old mod, unfortunately neither of those fixed the problem so I'm really at a loss now
EDIT: Ok so I'm having the issue with the 9mm as well now so I'm guessing other pistols that share the same reload animation as the 9mm have it aswell, need to find out how to replace sounds?
EDIT:Replaced the sounds with a mod(Realistic Gunshot sounds), didn't change anything though :/

Alright so its definitely not a mod as I disabled all of the mods except for the those ones and the problem still persists yet oddly enough, one of my sniper rifles had the issues with missing reloading sounds as well with all the mods disabled yet with them all enabled the sniper rifle has its reloading sounds back, so a mod is fixing the problem yet at the same time when I checked in FNVEdit the weapons themselves are not being modified or overwritten by anything else, also weird too is guns like the 9mm or Beretta added by fook reload with their sound just fine, and have the same reload animation so I'm even more at a loss, the sound files are in the folders for it too, I'd open up the GECK and see if I can manually do it somehow but I'm really unexperianced with the GECK and wouldn't know how to do such a thing, plus if it says in the GECK that it already has the reloading sound than it means that its something else possibly. Can reload animations alter the sound files used for the reload? I have Hitman's 1st Person Weapon Animation overhaul as well as Project Lazarus and Animation Project O.o
EDIT:I just found out that Project Lazarus and Animation Project was merged into a new mod called Solid Project and I'm going to update and let you all know if it fixes the problem, thanks for viewing this and giving me a place to get my thoughts down and brainstorm. ^.^