Spartan-IIs had the numbers on their armor when they got the first MJOLNIR - Mark IV. The Spartans you see in Halo Wars are Red Team, Spartan-IIs with Mark IV MJOLNIR. Spartan-IIs all had their number on Mark IV only.
Halo Wars takes place in 2531, whereas all other Halo games take place 20 years later - 2552 and later with never generations of MJOLNIR.
Look in other Halos that take place after Halo Wars - Combat Evolved with John-117 in Mark V, Halo 2 and 3 with John-117 in Mark VI. He never had any logos or his numbers. Nothing.
Some of Noble Team in Halo Reach had small logos on their Mark Vs - but not all. Only Jorge and Carter had numbers.
Spartan-VIs don't have any numbers, they have normal Service Numbers, which is not visible on armor. They often have Fireteam emblems... or unique markings.
If you're doing your own Spartan - go with whatever you want. If you want numbers or insignias, you're free to do whatever you want.
If you're doing a face character like Master Chief, it's generally better to stay accurate. Otherwise, if you change things, it won't be Master Chief anymore.
