@Sapemi, to be clear are you using MATE's Software Boutique or one of the other package managers like Synaptic or ...? If you are using the Boutique that is a curated list, not the complete list.
I used the package manager called Software (which I installed by using MATE's Software Boutique), to search for Netbeans & BlueJ. I found Netbeans, but not BlueJ. See below:
