I have heard the naming of the 404 to be in line with the popular 303 as Matt stated. I always have wondered if the 04 was a significant year in its development. Released in 1905 I always thought it made sense to be named as Jefferys 1904, 400 cartridge. The 404 Jeffery.
I am inclined to go along with this thinking as well especially if you take the circumstances and timing into consideration.
The British had a great deal of faith and likeing for the 303 by this time after it was introduced in 1888. As the 1898 Mauser became the benchmark for a hunting bolt rifle,Jeffery was working on a magazine rifle to replicate the double rifle 450/400 3 inch case and when the 404 was developed in 1904 there had just been the military exceptance of the 30-o3 produced in the US. There was a real surge in cartridge deveopement from the time that smokeless had been developed and there was enormous interest in both the military and civilian hunting sectors. The fact that it was a 30 cal of 03 must have been very fresh in Jeffery's minds and so the 40 cal in 04 would have been a natural inclination but instead of the 40-04 they gave it the name they did to possibly mirror the great exceptance of the 303 with the familiarity of the type of name ing rythem.
This is C&P from another source
"Jeffery did not have access to magnum length Mauser actions and had no choice but to use the standard Mauser action. In doing this he could not use the 450/400-3" case turned into rimless as the degree of opening up needed would have affected action integrity too much.
Jeffery had co-designed a shorter rimless cartridge by reducing the case length of his popular .450/400x3" case from 3" 76.2mm to 73mm.
This still marginally reduced the safety margin, but was sufficiently strong as long as the pressure was kept at the original specification of 17.2 tons per square inch (2,240 lbs to the ton). This considerable reduction in the volume of the cartridge case would have resulted in a drastic increase in pressure had they retained the .450/400x3" load and kept the same diameter bullet as for the .450/400; namely the .408". Jeffery worked through Le Personne with Krupp regarding barrel specifications as well as Eley and Kynoch who possessed the cartridge design expertise, to duplicate combustion space by increasing the case base diameter from 13.76mm/0.5417" to 13.843mm/0.545" and the shoulder diameter of the .450/400x3" from 13.233mm/.521" to
13.462mm/.530". The rimless version's bullet diameter was consequently increased to .4225". The nett result of the modifications to the .450/400x3" was the shorter, fatter, rimless cartridge we know as the .404 Jeffery and which used the weight of bullet and propellant as its rimmed predecessor."