I know one of the PCE's weakpoints was that 1 background layer that made it difficult to achieve parallax scrolling, but it seems some games were able to do it
like this part of dracula x
https://youtu.be/IV5TvOlKsj4?t=1h20m59s
or this stage of gates of thunder
https://youtu.be/oGguCcizT6M?t=28m24s
how could they do it, while say, ninja gaiden could only achieve a really choppy one?
That's a link to Lords of Thunder, not Gate of Thunder.
The PCE can do "parallax" style scrolling just like most 16bit systems; that is to say it divides sections of the background to scroll a different speeds. This can be done up to a single scanline to have the effect of "linescrolls".
What you're referring to is
overlapping parallax. And that's obviously something more complicated to do with only one background. Like others have mentioned, sprites are often used to small overlapping parts.
Just look at the Dracula X example you listed. Everything is made up of a single background layer as different speeds. Only the pillars holding the bridge are overlapping, and they are sprites.
But as you're probably aware, you can only have soo many sprites on a single display line before flicker or blankout happens. There's another technique called dynamic tiles. Lords of Thunder does indeed use them in some places, but definitely not as common as it uses sprites for overlapping parts.
One great example of dynamic tiles in Lords of Thunder, is the sand level wit the giant sand dragon/thing. The sand part is dynamic tiles and allows the dragon's "body" to move back and forth, independent of the multi-scrolling layers of the sand. This is achieved because the sand is a single column of 8x8 blocks, repeated across the screen horizontally. Each 8x8 block in that column is pre-animated to a full left to right rotation.
Dynamic tiles has a restriction on complexity; both size in storage AND the cpu resource to upload each update per frame. On top of that, sprites can be combined with them for an even more convincing effect (the sand Dragon in LoT does this; the head and tops of spikes are sprites).
There is another techniques, but they are limited. But when combined in certain ways - allows more complex scrolling. Back ground color scrolling is one of them (the first stage of Magical Chase), or character scrolling (Ys 3). Character scrolling is definitely rough, but at high speeds it can be very convincing if done right.
Ninja Gaiden on PCE tries to do
character scrolling, but messes it up
really bad. Normally, parallax designed around games designed from the ground up for the system - tends to look really good. Ninja Gaiden on the PCE kind of a budget title. Ignoring the parallax itself, the background tilework/art is actually inferior to the NES one which incorporates depth to the platforms with less tiles than the PCE (the PCE is fairly flat looking - lacking depth in the side view).