The challenge here is choosing/making rules that people like, that work, and that don't stifle creativity.
Using MOBA's as an example. You don't know what your opponent is going to take. You take a character and build set you feel comfortable with or that you think will work well in certain ways with other members of your team. However, if your opponent counters this, you can alter your build order to buy into abilities that combat your specific opponents to allow a suboptimal character to win out. In this way, MOBAs only feature soft counters instead of so-called hard counters. Taking an interesting character is perfectly fine since you can alter your build order to handle and counter your opponents.
In GoIO, there is no mid-match control. The only thing you can do is alter tactics to try to defeat a counter. Sometimes that just doesn't work.
Using Hephaestus Challenge as an example, I believe administration touched on this subject while ironing out rules. Some of the things in play with HC are experimental to see if the rules are clearly defined enough or if further measures are needed. Without a distinctly better solution, we left just a time limit to see if it would be sufficient, knowing that if/when season 2 happens adjustments can be made to account for problems.
Analyzing the problem, there are 3 possible ways to organize selections: timer/unorganized, simultaneous, or ordered.
Timer/unorganized is primarily what we have seen to this point. It relies on good faith and confidence to work. While it hasn't seen major problems, it is also asking for trouble sooner rather than later.
Simultaneous and ordered are the other 2 options. Ordered allows teams some form of reaction to their opponent. This means someone has to choose first, and someone gets to choose last. Major problems with this is that early ships are likely to be generic, which isn't necessarily bad, but somewhat stifles creativity. More unique ships tend to have more distinct weaknesses that can be taken advantage of.
Simultaneous has the same problem in a different way. Simultaneous selection, or blind, pushes teams to take more generic builds capable of fighting any style of enemy. Again, this isn't necessarily a bad thing, but it still stifles creativity.
Probably the best solution will come from a combination of the 3 options.
The key here is that no, to date it has not been a glaring problem, but it has the potential for abuse. Everything should be thought of in terms of scalability. If a serious event could be run for a much larger, not necessarily as friendly community, it should be able to run just as smooth as events in a smaller community. In that line of thought, this is a problem, and this is a good thread to put forward ideas to solve it.
A potential solution: Captains must submit the specific ships their team will be using say 20 minutes prior to match start. After all ships have been submitted, then captains will be informed of all ship choices and will have until 10 minutes prior to match start to submit their ship loadouts. When loadouts have been submitted, all captains will be informed, and all players will be invited to join the lobby with said ships and loadouts. Players may then adjust their personal loadouts until the timer ends to allow for soft countering of certain aspects.
The limited time for decisions is my least favorite part, and could probably be taken out in favor of a 3 day lead time for ship decision, plus 24 hours to choose ship loadout, allowing each team time to toy with how their ships will play against their opponent's ships.
So for example, Team A submits 2 Pyramidions and Team B submits a Goldfish and a Galleon. Both teams are informed of this. Team A then submits a gat-mortar loadout and a carrot loadout, hoping for quick kills and lots of disable on the heavy weapons, while Team B submits a lumberfish loadout and an asymmetric killing galleon loadout hoping to go for quick ranged kills by keeping the pyramidions locked down with lumberjacks. The teams then have time to practice against these specific builds playing for flaws, giving them time to find ways to avoid a "hard" counter. They join the lobby and are free to engage in a cat-and-mouse game of swapping ammo and tool personal loadouts prior to the match until the timer runs out and the game starts.
This allows teams to take interesting ship combinations knowing that if their ships are not favored the way they wanted to fly, then can pick weapons that help them combat their opponent's ship.