He doesn't know how things will turn out.

However he did knew that shadow is extremely dangerous and archer actively considers it a threat to humanity and not only that shirou knew about shadow being sakura since the first time he encountered it.he was just in denial ergo the responsibility of all the civilians who died by the shadows hand falls under shirou because he did not deal with the shadow when he had the change.

They are well past their prime productive period, and instead of wasting resources

that's an assumption since even if they can not be physically productive does not mean they can not be mentally productive since they still has more knowledge and experience than his son does and hence can cause far more development opportunity than their son could because of the son's lack of knowledge and experience by that metric the parents have far more productive value than their son especially with technology where physical work is not nearly as essential in comparison to mental work that could aid in development.

again the scenario does not provide the actual information of their worth.how good is the son both academically and physically alongside how skilled are their parents and in which fields do they work alongside what worth does that field have and many other information required to access that situation accurately.

basically your philosophical argument simplifies a very complicated situation which is not straight forward what so ever both morally and mathematically however under extreme circumstances like the distopian world (like miyuverse and notes) such philosophical argument becomes a necessity.the thing is even shirou has more awareness that sacrifices are required during extreme scenario and has to make the philosophical argument you proposed constantly alongside everyone else in those dystopia.the only reason we do not have to make those philosophical argument is because we are extremely lucky because of the rapidly improving technology which enhances our quality of lives.people during great depression era did not have such novelty and had to make those harsh decisions inorder to just survive or save others.

There is no objectively correct answer.

yes there is not however there are situations when you only have suboptimal and outright horrible choices present to you based on the situation and you have to chose an optimal choice regardless of how bad it may be since choosing nothing is significantly worse.the Black Death Pandemic is an example of that where because of the significantly inferior technology required them to perform extremely risky and painful experiments which sacrificed many lives however not doing that would have caused way more damage and way more death and those sacrifices were essential to control that pandemic and those researches were used till date abeit heavily refined.it is because of those experience and development that brought that we are not utterly screwed during the current pandemic as they were.