What is the ruling on the existence of suspicious messages to a colleague at my wife's work, and does the three-day period of prohibition apply if she does not clarify this?

We did not understand what you meant by your question about "the three days of prohibition" because you did not mention the words "divorce" or "prohibition." If you did not utter them, then there is no effect on the marriage. A woman's work in a place where she mixes with men is a gateway to evil and corruption. The husband must uphold his right of guardianship over his wife, protect her from temptations, establish Allah's boundaries in his home, cooperate with her in obedience to Allah, and have a good opinion of her.