Yes, Apple used 2.5" SSDs before the NGFF was ever a gleam in a Standards body's eyes. Here is a brief, and probably incomplete history:
Apple's prices on the SSDs are not cheap, but they are not using budget SSD in their computers, they are using top of the line or near top of the line Samsung NVMe NAND that would end up in the 970 EVO or Pro, not a Team Group or Silicon Power value SSD. If Apple ever decided to use 2.5" SSDs in their iMacs or Mac minis, you can bet it would probably not be a SATA 3 drive, (more like a U.2, but then what's the point), which is why I think they stick to spinning HDDs and Fusion drives until they can make the switch over to having a completely flash based lineup in the next 2-3 years.
- Apple used 2.5" SSDs beginning with the Mid 2010 iMacs (256GB only), but switched to blades with the Late 2012 models. Apple used 2.5" SSDs with some models of the MacBook Pro. I do not remember when they began offering them, but the last model to get them was the Mid 2012 15-inch and 13-inch (NON-Retina).
- Apple used non-standard 1.8" drives in the original 2008-2009 MacBook Air before switching to SATA and later PCIe flash blades, starting with the 2010 MacBook Air.
- Apple used 2.5" SSDs in the Mid 2011 and Late 2012 Mac minis.
- Apple used 2.5" SSDs in the Mid 2010 and Mid 2012 Mac Pros.
That being said, I understand that it can be a bit frustrating as something on the level of a Samsung 860 EVO or Crucial MX500 has Read/Write performance that surpasses the performance of the SATA blade in the original Mid 2012 Retina MacBook Pro, which still has good performance at this point (~300MB Write/~320MBRead) and still works fine for a lot of people who are still using one (me included). With a Samsung 860 EVO-based drive in a 21.5" iMac, a Fusion drive would not be necessary, although the average user would still have to deal with less storage than they get with an HDD or a Fusion drive, which is why I think Apple sticks with those configurations on the low end of the price scale to provide value for those users. Hopefully, NAND prices will continue to fall and Apple's investment in Toshiba will bring prices down for BTO options or at least higher capacity at the same prices.
I thought they used Samsung 830Pro SATA SSDs back in the day (alongside Sandisk and later Toshiba) from what I recall from 2011 Macs - very good quality and not cheap at all but obviously the usual Apple mark-up.
Apple at the moment are aiming towards captive NAND or custom connectors driven by the T2 ARM chip in more expensive models. It remains to be seen if Apple plan to add the T2 to lower priced Macs - if they do then I would suggest they have to mitigate the price of adding the T2 by switching to more powerful CPU.
A 2018 Mini with Iris Graphics 28w parts plus the T2 to control SSD would be an example - they might even go the whole hog and introduce a new case and with it free themselves to choose from a winder range of more powerful CPUs with the 2018 Mini. At the end of the day, by planting the T2 CPU in now they can add custom NAND SSD and also in future allow macOS to require a T2 CPU - making Hackintosh machines a virtual impossibility.
A 2.5" SATA bay in the next Mini would be great for adding storage, even better if it were user accessible.