Variety of factors:
Houston lost 4 high draft picks (2 1st rounders and 2 2nd rounders) for the sign stealing scandal.
Houston has traded away a shitload of prospects over the last 6 years.
Many of Houston's other pedigreed prospects (Forrest Whitley, Joe Perez, Korey Lee, Freudis Nova, Pedro Leon, Dauri Lorenzo, Collin Barber) have not had the kind of statistical breakout that was hoped/expected.
Because of the pandemic and evaluator laziness, many of Houston's best prospects were widely underrated. I noted in comment earlier today that Baseball Prospectus just had Gilbert, Clifford, Dezenzo, Baez, and Arrighetti in their Top 150, so at least one respected publication is catching up and realizing Houston's system is closer to average than terrible.
Houston clearly evaluates and develops pitching better/differently than almost every other team and doesn't target the same criteria that makes pitchers show up on prospect lists. We can safely assume there are dozen arms in their system that are not in anybody on the internet's Org Top 10 who will end up as solid MoR SP like France, Javier, Garcia, etc..
When Houston does have a good prospect, they promote them quickly. Most people expected Brown and Diaz to be in AAA most of this season.