The key may be in the age of director, who was born just after WW II, possibly in an area with limited or no indoor plumbing.
Even in the early 1980s, some Pairs hotels did not have a toilet in every room. I expect private houses were often the same, especially decades earlier. So, if a little girl (or boy) needed to pee or poo during the night, it was the chamber pot or hold it until the morning. And, peeing in a chamber pot is one thing; pooing is quite another. Try it! The pot has to be emptied and cleaned in the am too.
Also, there is reference to a governess or nanny, which is, again, old school. These women were hired to make parenting less onerous and intrusive on the parents- Children were pretty much required to be lifestyle accessories... seen, but not heard.
Given these things, I'm not surprised that a suppository was given and then the child's toilet routine done. The idea was that the suppository would make sure that they had a poo, hence empty their bowel, before going to bed. No messy chamber pot poos overnight.
I have not seen the film, but suspect that they were given the suppositories, rather than 'take' which implies self-insertion.
In some societies, pooing like clockwork is seen as a virtue. Sometimes, it is just naturally encouraged, sometimes imposed. Is there really much difference between suppositories at bedtime and a bowl of raisin bran or a glass of prune juice every morning? Either will ensure regular, fully successful, toilet trips at predictable times.