One possible match is Tachyon: The Fringe. I lack the wherewithal to provide screenshots at this time, but I will explain the rationale:
"between 1990 and 2000" -- Released in early 2000, right at the edge of your time frame.
"The game takes place in space." -- Yes. This is a space combat game, with light inventory management and story bits interspersed between combat missions. The player spends the vast majority of their active game time flying around in space.
"You have some kind of fighter that you control with the mouse." -- Yes, definitely. The game supported various control types, including joystick and mouse/keyboard. The game features 8 controllable space fighters (essentially, one of each type: light, medium, heavy, bomber), split evenly between the game's two factions.
"You navigate in space" -- Check. There's a lot of flying between starbases, asteroids, waypoints, gates, etc.
"fight some enemies or asteroids" -- Check. The player fights plenty of enemies during any given mission. Asteroids can be destroyed for fun and/or resources/loot, depending on the mission. The multiplayer game features a "Base Wars" mode devoted entirely to harvesting resources from asteroids in order to climb the tech tree, with the ultimate goal of destroying the opponent's base. Many, many asteroids get destroyed in this mode.
"retrieve weapons (dual red laser/quadruple green laser, etc.)" -- This is not a perfect match, but is at least a partial match. The "red laser/green laser" mention in particular strongly reminded me of the game's two factions, who have (essentially) color-coded lasers. The GalSpan faction has primarily green(ish) lasers, and the Bora faction has primarily red(ish) lasers. The heavier ship types can equip greater numbers of weapons, and the most powerful ships were able to mount 4+ laser weapons. The player spends a lot of time in early ships with only 1-2 lasers available, and getting to the "quad laser" ship certainly felt like a massive, memorable upgrade!
"and change levels by entering some kind of "stargate" by entering the vortex." -- Big match. The plot of the game centers largely around control of the gates connecting various systems, as a means of controlling independence, commerce, resources, etc. Almost every single mission requires the player to enter gates -- which have a big swirling Stargate-like central vortex while active -- multiple times.
"I had it on cardboard cd packaging as if it were an old game repackaged and resold. on the jacket they were a yellow fighter firing laser i guess" -- I cannot speak to the packaging itself, but this is a reasonable description of the game's box art. A blue/white GalSpan fighter is being chased by a brown/yellow Bora fighter, which is firing green lasers at their target.
Other possible matches include Descent: Freespace, and partially the X-Wing and Tie Fighter series. I won't go bullet-by-bullet, except to say that essentially all these same boxes get ticked in essentially the same fashion: released prior to 2000, space combat games, mouse controls, stuff gets shot, red and green lasers, and so forth.
The weakest part of this being a Descent: Freespace match (or X-wing, or Tie Fighter) remains that weapons are not collected mid-mission. One stronger item is that Descent: Freespace was repackaged in jewel-case-only format at least once by around 2000, because I acquired it that way first before acquiring the full-box version. Likewise, both X-Wing and Tie Fighter appeared, to the best of my knowledge, in paper-sleeve versions various software compilation packs (in various shades of "full game" and "demo" versions).
However, while Descent: Freespace ends missions by warping the player's ship out via a stargate-wormhole-like effect, this does not strictly match X-Wing or Tie Fighter.