No, it’s not intentional that level 1 weapon does more damage than a level 35 masterwork in identical circumstances. That’s a bug with the way their scaling system works.
It isn't doing more damage. The target has less armor/shield because you're attacking it with a level 1 gun/ability.
Level 1 cloudburst does ~224 damage per hit, MW Endless Siege doing ~3200 damage per hit(with the rest of my gear). The siege is doing more damage, the problem is that the mob scaling gives the target a lot more shield/armor when attacking with a lvl 45 gun/ability than with a lvl 1.
The numbers you see are real. The numbers you don't see are changing as you switch levels of weapon/ability. Which is exactly why you're not shown those numbers.
This is exactly what I'd expect with the type of scaling they've implemented. Just a matter of tweaking the curve. Is basically a graph with weapon/ability level on one axis, mob shield/armor on the other. One graph per difficulty level, with some mobs having individual modifiers.
Or I could be wrong.
I suppose another way to do this is behind the scenes instead of having raw damage numbers have percentage-based damage. That way nothing with the mobs is changing on the fly. Gun X at level Y does a fixed percentage of damage to mob Z at a given difficulty level and then you stack all the modifiers on top of that. That'd probably be cleaner on the back end but you'd have to change it on the player side so they could have traditional damage numbers to see.
As far as this particular imbalance goes, I would suspect that level 1 weapons aren't intended to have all the modifiers a fully geared player can stack on them, which means they'd need to be a higher percentage of damage for people using them at the appropriate levels to still get the job done. That'd be why they outclass endgame weapons currently when scaled for endgame content.
tldr; lots of theorycrafting based upon limited player experience.