I'm sure the 3 degree decision was pre-ILS era by quite some time. Pre-ILS is (roughly) pre-pressurization, 500-700 fpm is an ear friendly rate that gets the job of descending done in a reasonable period of time.
More likely the pioneers devoted some old-fashioned trial and error to this problem. At 5, 10 or 15 degrees they probably had problems engineering a respectable flare, especially with the marginal control authority provided by Bleriots, and whatnot. At 1 or 2 degress they probably noted that trees, telegraph poles, and smokestacks became troublesome obstacles.
The above is considerable conjecture, but I think 3 just worked.