Linex5 mode outoputs 1080 lines and cuts the picture on the top and botton. So it will also scale great on a 4k TV.
What I wanted to say (NTSC only) is, that in my case 3x looks as good as 5x, but only if you use the correct timings. 3x + Generic 4:3 + default settings looks way worse than 5x + Gneric 4:3 + default settings. It’s blurry and flickering that way. But with 256×240 Opt. and the correct timings it looks very good on my TV.
I have the same problem as you with my US Snes, otherwise I would still use 5x. But as 3x doesn’t cut the picture and is slightly smaller I changed all my consoles to it.