Note: the Guard Dialogue Overhaul SE mod also removes this warning (by default, after Alduin is defeated) and includes a bunch of other goodies -- I recommend at least taking a look at it instead.

This mod removes the "I need to ask you to stop. That... shouting... is making people nervous" warning or admonishment from guards in cities. No more will your whirlwind sprint be interrupted!

Other commentary (like "The Thu'um! He summons the Thu'um!", "Now that's a shout!", etc.) is not affected by this mod. 

How it works:

The mod adds another condition to the quest that manages the shout warning, WICastMagic03 ("Shout - Guard says stop"). The condition is false by default, so the quest never starts, so you never get a warning. 

You can disable the mod for a save by using:

set ShouldGuardsAdmonishShouts to 1.00

in the console. Note, this value persists across saves. Set back to 0.00 (the default) to re-enable the mod. Useful for testing.

Compatibility:

Mods that edit the WICastMagic03 quest will conflict. Since this quest is only used for the guard telling you to stop shouting, if other mods edit that quest, you aren't likely to care about it.

That said, I did import a fix from the Unofficial SSE Patch that makes guards not warn you about shouting in Calcelmo's museum/laboratory... which will only matter if you disable the mod as above, but I wanted to be thorough. The mod imports the fix and doesn't depend on the Unofficial Patch, but you should be running the Unofficial Patch regardless.