The non dirt-cheap part is converting all that material to digital. Someone would have to do the work and it's probably a lot of man hours. That has to be budgeted. In a world of dwindling return on music sales. Which has been an on-going trend for two decades. And they would have to sell that usage of money to share holders in said world of dwindling returns.
I can perfectly believe that they're that "stupid" to have them all in one place. I wouldn't say it's stupid so much as it's careless, but humans are careless. It should come as no surprise that we would exhibit careless behavior.

They've probably been saying for decades "one day now, we gotta hire someone to go through all that shit and save it digitally" "yeah man, you're right, but music sales are disappearing thanks to fucking spotify, we gotta put that off for now, next financial quarter, I mean it this time" fast forward twenty years and suddenly the fire hits "oh right, fuck fuck fuck". That would be the most human story of stories.
That has nothing to do with why there hasn't been a 2Pac album though. I actually think it's factually correct to say that online, there's been more leaks happening after the fire, than before. Granted, those didn't come from the masters, but so one thing we know is that Death Row (the new Death Row, while Suge was in jail the second time and before the murder trial) had an FTP server with a copy of like every track they had access to. That was a reference server, but we also know a lot of acapellas were sent to DJs and to Koch by both the estate and Death Row, so digital copies of acapellas are out there. We also know some acapellas are available in layers. So if not every Tupac song, at least many have been turned to digital as part of processes when albums were released. Like for instance, they remixed like 80 tracks for UTEOT, and some of those remixes ended up on BD. Who's "they"? Well, a lot of different people. A lot of tracks had several remixes done of them, and then Afeni would pick the one she liked. Acapellas in layers flying left and right. If they lifted them from the masters, in layers, it stands to reason that they got the instrumental tracks too. It's a cumbersome job to transfer analogue to digital because you have to play on one device, record on the other, and just wait while it plays at 1x speed. If you were gonna do that, wouldn't you just make sure you grabbed anything on the tapes so as to never have to do it again? It's not perfect logic, but that's how I would reason.
What all this suggests to me, is, there's probably digital Tupac material left even if the fire took some Tupac stuff out. Also, I'm not sure why but I have this feeling. There's a difference between master recordings and master copies of released albums. When an album (which consists on songs that were recorded to several master reels) is compiled, a master copy of the album is made for production. Something about the wording in the text gave me the feeling that the storage was a storage of such album masters. They're called "red books" and is used in the copying process of CD albums. If it's the case that the facility stored red books, that means that the master copies of Tupac's albums could be gone, but the master reels with the songs on them could still be stored somewhere else. When Pac was on Death Row, Death Row had the masters, they weren't sending them to a storage somewhere. Remember that story of when Pac tried to get his master with him out of the studio and Suge wouldn't allow it?
The wording in the article sounds layman enough that I'm not sure the journalist is attent to what kind of masters they were storing there. I could be wrong of course!