I believe that these soft counters to a certain extent, can be reduced by a whole lot as long as players are watchful. They have to be wary of the possible hard and soft counters and do their best to avoid them.
Scouting is one of the minor aspects of an RTS game
You're being too modest. Scouting is a critical element of any decent RTS. It is generally impossible to win against a decent opponent without scouting (and scouting isn't just checking out their base at the start of the game to see what their build order is). You need to control the map, which means you need to know where units are concentrated at all times. The SC2 Protoss Observer is a very dedicated unit for that, but most games do with "secondary" scouts. In Age of Empires II, most civilizations start out with a weak cavalry whose speed makes it ideal for scouting. Players using it as an offensive or defensive weapon in the early game generally end up losing strategic advantage after its death. While it can harrass peasants and really be a nuisance to your opponent's tactics, its best used as a silent observer. Information has a value, and most player tend to forget this. It is oftentimes the major difference between a pro player and a good player. In SC2, a lot of Diamond player are highly skilled but not so efficient at getting sufficient information. In other words, they have conditionned their mind to analyze data and come up with the appropriate solution, but they just don't get enough data by lack of scouting.
Yeah, scouting has to be a continuous effort and not just sending a scout unit at the start and playing blindly for the rest of the game. As the saying goes "know your enemy and know yourself and you can fight a hundred battles without disaster." You have to know what your enemy is up to in order to plan a strategy to counter theirs. You will also not be surprised as you know what your opponent is up to. It also gives you time to think of what you can do if the enemy comes instead of some last minute notice which will test crisis management.
Even though mechanics can be your life saver as seen in many pro games, at the same time, if both players have the same level in terms of mechanics, this is where wits will come in place. Whether they are meticulous enough to scout the whole map to check for any possible surprises(Hidden collection of resources or proxy bases) and prevent them from probing into the base. In this type of occasion, it becomes an intel war where the one with the best scout have the better chance to win. However, intel war can also be a war of deception. In some pro games, the moment the enemy scouts their base. Instead of proceeding with that strategy, they will go for another build which are strong against the defense built against the previous strategy. This is also the beauty of RTS games in my opinion. A complex game that requires the mastering of many different aspects.