RS,
Thank you for sharing your personal experience, but as I see it, your main point, having explained the issues, should merely be to make Shugdenpas aware of these potential circumstances and to be careful. Your valuable information should not result in the broad-stroke conclusion that there's no such thing as relying in secret, which I have already refuted by telling you I know people who do so.
What you discovered in your experience could be the result of magic attack, or the Protector telling you personally to distance yourself from people with broken samaya, wrong views, wrong intentions, and wrong activities, all of which may have been rubbing off on you, like cigarette smoke!
I understand some of the subtleties you speak of, but it is also the experience of myself and others that secret devotion can be kept secret AND protected by doing various things with concentration. Beyond not giving any doorway for others to recognize it (as you did), you can close the subtle doorways with weekly Kangso, Trakze retreat, Migtsema recitations and armor, recitation and meditation on the Vajrabhairava command wheel activities and his mantras, Yidam armor mantras, and very powerful experience of love, compassion, and wisdom realizing the two truths. If we can't do this, it is very possible, as you've explained, that you will be affected through close association with negative energy. Keeping a good heart is great, but we also need to become aware of subtle influences an know if we're being adversely effected.
There is a such thing as relying on Dorje Shugden secretly, but not everyone can do it amongst anti-Shugden people without consequence.