Is it common for humanitarian flights to lack security control for the baggage?

You were on a military (or State Dept.) flight.

This would have been a lot more obvious if the airframe had been haze grey and an Antonov-124 and had military logos on it.

But the fact is, a lot of military flights fly with leased civilian equipment. Usually this is third-tier civilian fleets like cargo planes (e.g. Kalitta Air), but in the current regime, several things are true:

• First-rate commercial airlines are happy to take any business they can get.
• Governments would much rather hire them than subsidize them, because subsidies are political third rails, and big treaty issues.
• Logistics people are happy to have an actual passenger airplane instead of having to improvise with a cargo plane.

I drive by a USAF logistics base from time to time, and there are constantly large airliners of a variety of marques and nationalities in there, or just unmarked white-tails. They are deploying or returning troops. The US uses this same infrastructure to repatriate citizens for COVID-19, and brings them into those same logistics bases.

Mind you, the flight was probably arranged by your State Department aka Foreign Office, i.e. the diplomatic corps who run embassies, haggle out treaties, help developing nations, issue visas, etc. Same deal; they're contracting out to get an aircraft (probably "wet" i.e. supplied with airline crew and support). If anybody can talk a foreign nation into lending use of a military base, it'd be your country's State Dept.

If it wasn't a scheduled commercial flight, then different security rules (or none!) may apply.

I don't know what country you were in, or what the nature of the flight was (as you didn't specify), but it sounds like you took a flight which wasn't a scheduled commercial service. (Even if it is a major carrier and has a flight number, it still might not be a scheduled commercial service.) In many countries, entire sets of rules don't apply to such flights.

For instance, in the US, such a flight might be considered general aviation and fly under Part 91, and neither the passengers nor baggage would have to go through any sort of government mandated security procedure unless it was flying into Washington, DC.

A whole risk class does not apply.

The main risk is somebody hijacking the plane.
Hijacking takes preparation, which doesn't work too well on an ad-hoc flight.
Even if a potential terrorist happened to be in the group eligible for the flight, they are unlikely to have weapons or bombs easily accessible; plus it's likely that they will be accommodated in some central place because they have to wait for the plane to actually arrive, and it's easier to monitor them for suspicious behaviour in that time.

So you are eliminating a much smaller risk than normal if you insist on searching the baggage, and as long as nobody manages to actually sneak a bomb on a humanitarian flight, authorities are likely to leave it that way.

And that's likely also the reason why regulations are much more relaxed.

Luggage doesn't appear to be a major concern in these situations, compared to triage, crowd control, interfacing with local authorities, etc. If anything, you're more likely to be searched when reaching the collection points than just before boarding the plane.

This doctrine document from the French military doesn't mention anything specific regarding luggage but this dossier does include pictures of soldiers sifting through a suitcase and searching people in Rwanda in 1994 (p. 23).

Generally speaking, there is nothing magical about X-ray machines or having electronics on a plane. To the extent that regular procedures serve a purpose, it's also through deterrence and reducing (not eliminating) the risk someone might a laptop to hide a knife to hijack a plane. But it's only one risk among many it's entirely reasonable to mitigate it in other ways or make other trade-offs, especially in emergency situations.