The reason is that they’re a problematic source. Everyone’s also being much more cautious since the al-Ahli Arab Hospital blast because several major news organizations had to apologize for uncritically reporting Hamas/MoH claims that turned out to be false.
I’m sure first responders report numbers to the ministry but you’re wrong to think that they’re reporting to you. The voice that speaks through the ministry is Hamas. You’re taking it purely on faith that it’s otherwise, but it ain’t true just because you’d like it to be. I’m not sure Hamas has really earned your faith. They’re being widely reported because, as you said, there’s no one else in a position to report. But best-we-have doesn’t really mean good, does it? And it shouldn’t mean that we stop evaluating them critically as a source.