First of all, I would never put all my eggs in one basket. 5000 rounds is a lot, especially if you are considering a shelf life of 10-20 years for those rounds. I would never load and store a year's worth of one caliber of ammo (and I actually averaged 10,000 rounds/year for a stretch of about 8 years). Even at that, I only kept around 1000 rounds loaded per caliber at a time. If all you have and all you will ever have is 9mm, I guess you can load 'em all up, but that's tying up a lot of primers and powder that can potentially be used in other calibers should you buy some more guns. I suppose if you can afford it and have access to more primers at the drop of a hat you're OK.
I've done testing with powders and PC. I already knew that high nitroglycerine content powders like Titegroup, Power Pistol and Bullseye ate away at some powder hoppers if left overnight or over a week of reloading. My Hornady LnL AP hopper is dark brown just from the contact of pouring dozens of pounds of powder for just an hour at a time during a loading session. I had started a multi month test of powders sitting against bullets coated with the old Harbor Freight Red powder. I've lost some of the pictures and got rid of the samples after a couple of years because I figured I don't keep loaded ammunition that long anyway. I usually shoot everything I load within a couple of months.
These were the powders I had on hand at the beginning of the test. In fact, I knew Clays, Unique and Red Dot had very little to no nitroglycerin in them while the others (Bullseye, Titegroup, Power Pistol) had a lot of NG in their double base. The rest of the powder sitting in the case was not discolored, only a very small amount of the powder coat on the bullet base was distorted. So my conclusion was that the NG did interact with the PC but it was just a fast surface action at the point of contact and not a progressive interaction.
I've shot the same loads with "older" loads of a few months using PC and High Nitro powder and could not distinguish them between those and new loads. So there seem to be no major change within a few months. I cannot say what would happen over many years because I have no intention of loading a bunch of rounds, setting them aside for years and then shooting them so if you want to empirically test this yourself, you are welcome to do so.
The safest route would be to load a year's worth of rounds using a low nitro content powder such as Unique or Universal.