I am considerring buying WC 1+2 bundle but read some reviews that said that the game tends to slow down to unplayable speed when there are many shps on the screen. Anyone knows if GOG did fix this?

Can't be fixed, it's inherent in how the game works. You can configure the DOSbox cycles to have the speed you are more comfortable with but that's how the game is.
It's one of those games that runs as fast as the CPU does regardless, if you eliminate the slowdown the game will run too fast to be playable.
They did make a reprogrammed version for windows (not available on GOG) that doesn't have this particular issue but it's extremely buggy, there is a modder on Wing Commander CIC that is trying to correct the issues but at this moment it's still incomplete IIRC and you'd need to get the Kilrathi Saga version somewhere else to mod it.

I'm also having a lot of trouble with this. It's wrecking the game for me.

Have you tried upping the CPu cycles a bit? There should be a text file you can modify in the game DOSbox folder.

Just be warned that if you raise them too much the game will play too fast.