Thanks to Sprigellania's video with 100% accuracy, we now have confirmation that the AoE hits from ion railgun do not count as additional hits for accuracy.
To ensure that I did not miscount, I recorded in a spreadsheet, for each shot, the time and flytext damage.
I counted 50 shots fired, 3 of which were ion railguns which also hit other targets with the AoE effect.
If the hits from ion AoE counted as separate hits, there would be 58 hits recorded; if not, 50 hits.
The scoreboard showed 50 hits, consistent with AoE hits not counting.
As a check, summing the damage from all hits gave 70637, 4 less than the value of 70641 shown on the scoreboard, well within expected rounding error if the game rounds flytexts, but not an internal damage counter.