I thought about this for one of my upcoming projects, too. Seeing as though the body armour and personal kits in-game look similar in some ways to an EVA suit, you could tell the player to "make it visible" for the duration of the mission - sending them to a shuttlebay or transporter room to "suit up". You couldn't police it, nor make them do it, but it's the only work-around I could think of.
One of my missions, "The Infinitesimal Frontier," involves a situation that logically would demand an environmental suit. (I've even read reviews from players who complained about the lack of them!) Until we have EVA suits, however, you've got to find creative ways around this.
Fortunately for us, Star Trek: The Animated Series faced its own technical constraints and gave us all an easy out that conforms to established Trek lore! My mission contains dialogue that indicates the personal shields used by Starfleet personnel in the time of Star Trek Online can be modified to operate in the same was as the animated series' life support belts.
You can bet that if I had access to an environmental suit, however, that your away team would be using it in my mission!
I have seen some creative reasons why I do not have a suit in some dangerous situations.. mostly they revolve around a some sort of techno reason why my existing shielding has been upgraded, or I've been asked to enable the visuals on my armor etc.
Until we get suits (likely a Featured episode thing imo) we'll just have to rely on our creativity as authors and the patience and willingness of our audience.
Wouldn't surprise me one bit. I hope not though. I don't think it would be that hard, they have been throwing new costumes in every few weeks it seems. Imagine how many sales they would get if it was a C-Store item. lol