I said widely collectible, there will always be people collecting them just as people did before it became the cool mainstream thing to do. Even with beanie babies some people still collect them, and some are actually still quite valuable. It's just that now the majority of them are basically worthless or near worthless as most people only buy them for cheap to have a cute bear on display, not really to collect them anymore.
I remember around 2000/2001-ish Atari 2600 games became somewhat popular to collect, even common games could be sold for $2-$5 each. Now good luck getting $1 for a common game, most people moved away from collecting that console except for a few collectors and it's just the rare games that have significant value. Barely any collectors I run across actually collect pre-NES anything, Atari, Coleco, Intellivision are all basically ignored by most collectors now.
Here's my opinion, if something can be found on ebay at any given time then it's not that rare. Most valuable NES/SNES games are listed on ebay at any time, even if the prices are listed high they're still easy to find and available for purchase. Copies are still selling and more copies are being listed every few months, they're really not that rare compared to other collectibles. For example with actual rare stuff related to VHS tapes and laserdiscs, I have several where copies only turn up once every few months or even years, yet most still barely sell for $10-$30 when they are actually available. Value for anything really just depends on demand, something being rare isn't enough. If games aren't collectible in the mainstream anymore then the value will just drop as they're still too common to find. For most people dealing with original hardware is more of a pain than anything as most people don't have the correct TVs to even play them, using original hardware requires buying various converters and dealing with various shortfalls like having no working lightgun games, and with age more hardware needs to be repaired or maintained just to keep running. Eventually most people besides the die hard collectors will give up and move on.
I mostly hate pirate carts that look near perfect to the originals, I'll make exceptions to multicarts just because they're a neat oddity and of course translations or unreleased games are a bit different. I'm pretty sure someone released an alternate version of Streets of Rage 3 with added content a few years ago and it was available for purchase on a bootleg cart from a source, though I could be mixing it up with a different game instead. Old pirates from the 90's looked odd and were pretty hard to mistake for original games, they're still neat oddities to keep if found cheap. Straight modern pirates just irritate me and make me reluctant to buy anything I can't look over in person.
I'm not sure if bootlegs are specifically why those specific DVDs are cheaper. I thought that the Matrix of Leadership was reprinted or more widely available at some point, that's why it's cheaper now. It was in more high demand when the Transformers movies were starting to come out but now it dropped because the interest in the films dropped and the sets are more common to find. The GI Joe and Real Ghostbusters sets are harder to find and that's why they're so expensive now. I personally was waiting for the Real Ghostbusters set to drop in price before I would buy it but that never happened. Oh well. I've kind of moved on from older cartoons anyway so I'm not buying as many sets these days. Just wait until these series get released on Bluray, then the value of the DVDs will drop. As formats for video keep changing the older ones will get less valuable as long as they get re-released on the newer formats. Nobody would have thought their VHS tapes or laserdiscs would have become so worthless, people spent so much on these when they were new.