This shouldn't be too much of a problem. People will probably trust files uploaded on the Nexus page more though.
I must say, however, that NV Nexus has a nice file setup.
I'm curious as to why you want to put it on your own site. Nothing wrong with it, just wondering.
*In a deep voice* My files will maintain their purity by being uploaded to the site of cleanliness.

*j/k*
*serious*
Personally I just upload to my site since it's just there and i'm not using up that much bandwith. Instead of bogging down the falloutnexus site with the files of an unknown modder I rather put them up on my site. Maybe when I get some downloads and feel that my project is worthy of being advertised a bit more to the general public i'll upload it to the nexus site. Maybe consider this a closed beta scenario with limited release for testing.
Already drawn up major plans and feel that I can "Possibly" put in a more unique crafting system similar to other RPGs where you have raw materials, sub-components, components, and main materials. One thing i'll also be looking into is changing the actual food/water items so they have more unique effects in HC mode. However that project will be incorporated at a later date with the crafting system being my main focus.
On a side note I did find something interesting poking around the weapon files with the Weathered 10mm pistol. Apparently it looks like developers were intending to add in the ability to upgrade the item with a silencer, extended magazine and a laser site. However models for the item were never created to begin with which is why we see the square/triangle thing with the exclamation ! point. The only *Fix* I have in mind for this from what i'm seeing is to go to the mod section and select "None" on all of the mod options. This will prevent the gun from being modified by the stuff similar to how the unique items like the Ratslayer and La Lounge Carbine aren't modifiable.