Well, your 3rd gear is not 'missing', if the gear cog was broken or such, the noise would be horrendous.
What it is usually called is 'a false neutral'. A spot between all gears that doesn't quite engage correctly.
1. This is the main culprit on a Ducati, YOU, especially the older ones with lots of miles. Often the fix is quoted as "Shift like you mean it".
2. Some say clutch adjustment not correct and dragging when clutch lever pulled slowing the change and not quite engaging.
solutions offered range from bleeding clutch and checking lever play etc. etc.
3. The selector shaft is bent, or centering spring broken, yes, can happen. In my experience though, you would have false neutrals between all / any gears 1-2, 2-3. etc. etc.
4. If only between one particular set, as you mentioned, I have found it to be 'out of adjustment'. I have looked closely at this years ago and we found the distance between positions on the internal selector drum slightly longer between 2-3 and 3-4. and is the usual spot for 'missed gear changes'. It is not an issue if the fork / spring assembly is correctly adjusted. In the late 90's, we did a lot of warranty fixes for the false neutral problem. In all the ones I did, it was bad adjustment. Mainly though, The salesman at the shop raced a Ducati, hitting a false neutral on the track was dangerous and we spent some time looking into it.
Before tearing into the alt case, just try changing gears with a bit more force, when changing up, hold the pressure with your foot until the clutch is released, don't just stab it. Most times it just needs a different riding style. You won't break anything.
If you decide to go in, here is a diagram of what it all looks like.
View attachment 230177
24. is the arm that moves the gears, there are marks to set this to a central position
20. is the spring that keeps it engaged, but allows it to 'ride up' between gears.
33. is the adjuster plate, two bolts, and you can see the holes are slotted to allow adjustment.
If it's out of adjustment, the arm does not fully extend in either direction, giving a false neutral.
here is a picture of the selector drum showing the 'grooves' to move between gears, well some of them.
The selector shaft rides on the 'wider' part on the right, and either, pushes or pulls the pins to rotate the drum.
View attachment 230178
For more insight, just search, "Ducati false neutral" It's quite common.
Hope this helps.