If you're overplaying players with low fatigue, then I can understand managers asking "why".
I am currently managing an NT side. Knowing the frustration of this full well, and having complained about it numerous times, for all of the NT squad I complied a list of their teams and their home match time preferences and set the times for the NT home matches based on giving the most rest time between games as possible for the players, taking into account the endurance of players in the squad.
Difficult to do it for away matches as the times will differ depending on who the club side is playing but I do check before each NT match and tweak the teams if it appars a player will be severly impacted.
It's time consuming, but knowing just how damned frustrating it is to have some selfish clown killing your best players, especially true of goalkeepers who tend to be older, instead of using the squad (and appreciating the affect of fatigue on attributes in the first place).
It's not always possible. Sometimes the system throws up impossible schedules, sometimes the ME will screw planning up with an injury and unplanned substitution, but by and large I see it as having a responsibility to the club sides as well as the NT side. It's a two way street.
If a manager were to ask me not to play someone in a particular match because they had an important game, I'd certainly take it into consideration and try to alter my team/formation in a way that doesn't impact club or country.
It's a shame the developer is MIA and nothing is going to change. I found a way of preventing my players being killed by the worst NT managers but was sanctioned for it. Worked out quite well because I found another footy game (I won't name it because of forum rules) which I'm enjoying as much, if not more, than RS. A lot more simplistic in terms of club building but the match viewer and tactics options are superb (with in match tactical changes, live subs, individual instructions to players, not limited to certain formations if you want any success and, importantly, a developer who still gives a damn about his game).