I have the complete US released DS9 laserdiscs. I also have some TNG episodes. I am also going to get some(or all) X-Files LD soon. I see there are japanese boxsets of these shows. Could anybody tell me whether these boxsets are superior in terms of picture quality?

I can only comment on the X-Files, I do have the US versions & Japanese LD Boxes,

Picture quality related, I would say there is no difference (most US versions are pressed by Kuraray in Japan, which have an excelent picture quality, the Japanese are pressed by Pioneer JP).

The US X-files LDs do not cover all episodes, it is a sub-set of Season S1 (12 out of 24), S2 (12 out of 25), S3 (12 out of 24), S4 (6 out of 24) and also the sequence of the episodes is out of order.

The japaneese boxes contain all episodes from Season 1 - 7 (unfortunately there are no extras), but very nice boxes, sleeves & episode guides.

The US versions contain on the other hand an intro for most of the episodes which is not present in the japaneese box set.

those japanese box sets cost an insane amount of money

For the Star Trek episodes, the picture quality is the same, except the Japanese versions have subtitles in some spots. Primarily they are no subtitles as the titles are Bilingual (English on Digital Tracks, Japanese on the Analog tracks). The entire TOS series (3 boxes) and TNG series (14 boxes) are available. Only 5 seasons (10 box sets each) of DS9 and Voyager are available in Japanese box sets. Episodes from TOS in the Japanese box sets may not use the correct opening credits sequence, as the seasons aired much later in Japan - so season 2 or 3 openings may exist on season 1 episodes.

There is one episode from Season 7, "Sub Rosa" which is missing footage from the US release. The US release of this title has been shortened by nearly 4½ minutes. The entire 2nd act, which should begin after the first "commercial" break (minute 14:17 on the side) is missing. The program skips the entire act, picking up after the 2nd "commercial" break. This accounts for the shortened running time. I made Pioneer aware of the problem and after some investigation determined that the tape provided by Paramount was faulty. A corrected tape was provided to Pioneer with instructions that should a repressing of the title be necessary, the corrected tape was to be used. The disc was never repressed.

All the japanese Original Star Trek episodes were got from 16mm prints and it shows. Also every single episode has subtitles burnt in at some point during the episodes. While the USA prints were sourced from 35mm, they have a colour problem on most episodes which is only corrected by having an X9 or S9. While the packaging is superior in the Japanese versions the episode presentation certainly isn't. The Japanese pressing of The Next Generation are most certainly superior to the USA pressings with richer blacks. Again like DS9 and Voyager, they don't have burnt in japanese subtitles except for a couple of times to explain signs in the background. All the japanese pressings have laserdisc graphics so if you have an S9 or X9, you can excess them.
For SD pressings the japanese pressing are easily the best versions of DS9, Voyager and Next Generation to get.