Turns out this is a lot more complicated than I ever dreamed. The Simpson catalog in fact specifies 10d nails that are 3 inches long, and allows 10d nails that are 1-1/2 inches long for certain hangers, but as near as I can tell only for the header nails, not for the joist nails. For many of the hangers, the correct nail is the 10d 3 inch long nail, or for some of the heavy duty hangers 16d nails are specified.
Here is where things get odd. Simpson has a load reduction table that specifies the reduction (typically to about 70%) if you substitute 10d 1-1/2 inch nails for 10d 3 inch nails. However, there does not appear to be a reduction table for using the shorter nails into the joist. As near as I can tell, Simpson does not want you to use the shorter nail into the joist, so they don't provide a table showing required load reduction if you do use it. I guess this means that Simpson is not going to tell you what reduction to take if you inadvertently use the shorter nails into the joist.
The strange thing is that at Home Depot, Lowes etc. the short nails are sold as "joist hanger nails", and you have to search the hardware aisle for three inch hot dip galvanized nails that meet the spec of Simpson and will withstand PT lumber. This probably explains why the majority of decks are nailed together with short nails, which by the way are easily identified by the 10 stamped on the head of the nail. I can't recall ever going into a Big Box store and finding 10d three inch nails next to the hangers, so this probably explains why hardly anyone uses the proper nail to put up a hanger.
All that said, the load capacity of a nail in pure shear has little to do with the length of the nail, and everything to do with the diameter and strength of steel. However, the Simpson catalog lists load capacity for floor loads (nearly pure shear on the nails), but also for uplift and seismic. Under seismic loading, nails may be subjected to pull out forces, and the deck could be subjected to torsional forces, neither of which are pure shear, hence the length of the nail could be very significant for that specific type of load. A similar argument could be made for wind load, as the deck could be subjected to twisting loads, and individual nails could be subjected to pullout forces. You might also make the case that short nails are more likely to get loose over time as the wood shrinks and checks.
Obviously the proper thing is to use the specified nail, however you already used the wrong size. The hanger capacity could be downrated to the Simpson value of approximately 70 percent for the header nails, which is probably well above the required capacity anyway. The issue with the joist nails is more complicated, since Simpson does not publish a reduction factor for the short joist nail.
I suppose you could pull all the joist nails and use longer ones, and compute the capacity at 70 percent or so. This is probably adequate, but can be checked. Pulling the nails is likely to be a PITA, but since the joist nails go through a tab, it might be doable.
Alternatively, you could leave the shorter nails in the joist, and take your chances, if the inspector lets you do so. If you don't live in seismic country, and you manage to avoid hurricanes and tornadoes, my guess is you will be just fine. However, I am not your local inspector, so my guess carries no weight.