A Matter of Opinions
Why such a debate over making changes to a game client? Why would some people embrace their use while others despise them and call for their complete eradication?
Answers to these questions are not easy to track down and the debate rages on amongst forum posters and modders, professionals and amateurs alike. On one side you have the people screaming that modifications like the Thunderbringer's Ult Warning mod are unfair and put those without them at a disadvantage.
On the other hand, you have those who embrace things like BardUI and the Bang! Mod pack to give them the information they need in a superior package to what S2 currently offers the community in their default UI. But who is right and who is wrong? In what might be a twist of fate, neither side can truly claim victory because the only ones who have the final say are the developers.
S2's Official Statements on the Subject

This is a vague policy at best with a complete blanket ban on a little used mode that S2 recently implemented to help with tournament play. While it does shed some light on the issue with a quasi-official stance, a much more involved posture would make more sense, especially in light of many tournaments not requiring Tournament Mode to even be used.
Perhaps highlighting the biggest problem with this policy is the simple fact that just about every person that would use modifications plays their games in either matchmaking or through the public lobby, thus entirely avoiding this policy all together.
Unless a wider reaching modification policy is put in place it would seem that S2 is almost condoning the use of any and all modifications for casual play, which could prove disastrous as people create modifications that create more and more controversy among the casual player base.
Mods Not All Bad
Still, modifications are far from all bad. In fact, sometimes they highlight areas where the UI can be improved and their widespread use creates a situation where S2 fast tracks implementation of a similar feature into the game itself.
One particular mod of note that, when perfected should make the appearance of the micro-heavy heroes a lot more common is Bangerz upcoming "Control Freak" mod. This mod promises to greatly enhance the functionality of the client to allow for things like permanent control groups tied to specific heroes such as Ophelia or Balphagore, which allow for quicker reaction times when using their minions, and also the ability to issue attack move orders and map minion's abilities to hotkeys without having to select them.
It's functionality like that that proves that modifications aren't all that bad since so many people find it extremely challenging to micro in the current UI and therefore heroes with great potential like Ophelia and Balphagore are not played nearly as much as they could be due to the challenges associated with their use and the limitations of the current UI.
This debate will continue to rage on until S2 Formulates an official policy on what's acceptable and what's not in current game-play so that mods like the Last Hit Assist and the Valkyrie Christmas Tree Arrow modifications can be officially commented on as to whether they are allowable by the S2 staff.
As always, we'll continue to bring you any updated coverage of S2Games' modification policy as well as any news regarding any interesting new UI mods that might be coming down the pipeline.

Links
Modification Central - Links to Bangerz Mod Pack
List of HoN Mods Currently Available - The Official Forum Section