Yeah, such a missed opportunity but who knows may be Sonic Team / Gamefam did want to reference it to Shinobi but SEGA didn't allow it.
Remember, SEGA didn't allow Joe Musashi to be a secret playable character in Streets of Rage 4 when the developer proposed it.
Well, not like SEGA rejected it, it's more like they didn't say a yes so it couldn't be done.
Same reason with collaboration. It couldn't happen if the big bosses at SEGA didn't say yes.
In a way, I could understand why Joe Musashi was not in SoR4. Whenever or not Streets or Rage and Shinobi take place on the same Earth or not, it would likely have been confusing if he cameo in the story. Maybe as a reskin or unlockable character exclusive to Arcade or Survival.
Also, Roblox is... Roblox. Sonic Speed Sim has it's own isolated continuity from the main series of games so they could get away with crossovers.
And heck whenever they want human Sega characters looking like Roblox avatars or not, that's their choice.