Pre-458 F1 transmission cars have largely turned the corner on depreciation. The current macro-scale car market correction notwithstanding, even formerly undesirable models are stable. In some cases they have appreciated- looked at F355 prices lately? F1 cars have increased, although like you mention 6 speed cars are much higher.

As far as the repairability of F1 transmissions, it's important to keep in mind that these are essentially 'automated' versions of the manual transmission, not conventional automatic transmissions. There's no torque converter, but there is a clutch like a regular manual. The parts that fail are not usually the expensive gearbox internals (which Ferrari is pretty good at), but rather the bits that automate the operation- pressure switches, hydraulic pumps and solenoids- and the clutch. These can be replaced and there are aftermarket solutions and parts-bin interchanges to fix this stuff.

One mistake folks make with F1 cars is driving it like an automatic. Because the F1 gearbox is fundamentally an automated manual gearbox, driving it like a conventional automatic will cause premature wear. For example, creeping along in traffic or while parking is totally fine for a car with a regular auto trans, but in a F1-equipped Ferrari it will engage the clutch over and over again, slipping and wearing it in short order. This is partially a failure of interface design, as an F1 car will 'let' you drive it like an auto with little warning until you need an expensive clutch service in a couple thousand miles. This accounts for some of the bad reputation of F1 transmissions, as people drove it like a regular auto and racked up big service bills immediately.

The second big mistake owners make is expecting a Ferrari dealer to service an older F1 transmission. First, they don't retain institutional knowledge and support of older systems, which means techs don't know them very well and official parts availability is bad. Second, dealer policy is usually to replace the entire transmission if there is a fault. They won't do the diagnostic work to figure out if it's just a switch or some other component fails. This creates a situation where the best outcome is paying an exorbitant amount for a new F1 transmission, and the worst outcome is being told the transmission is no longer available from the factory and being left with a dead car. Instead of a dealer, anyone with an older F1-equipped Ferrari needs to be working with an independent specialist that is familiar with these cars. Even if you need to transport the car a couple hundred miles away, it will likely cost less compared to the dealer. Good independents will know these older systems better than dealer techs and be able to try solutions that dealers won't consider (such as replacing/adjusting component parts or sourcing used parts to replace parts NLA from the factory). Their labor rates and parts cost will also be lower.

All that said, yeah build quality and durability have never been Ferrari's strong suits. Porsche has always been the sensible supercar choice. However, there are ways to improve the old Ferrari ownership experience and all of them start with getting the car away from the dealer.