The NHL Draft can be tough since guys are first time draft eligible at 18. Not everybody's in a position to shine at that age. Goaltending in general can be harder to scout than say a point scoring forward. Most goalies aren't sniffing at an NHL spot until they're 23-24.
Lundqvist was playing in the Swedish junior league whereas Mikael Tellqvist and Stefan Liv (RIP) were a year+ older but had some starts in the senior league. Somebody like Ilya Bryzgalov went in that draft but that was his third time being draft eligible. Perhaps not coincidentally, that was the year Bryzgalov was promoted to the senior club.
Looking at Central Scouting's list from that year and they had Lundqvist listed at 5'11. So perhaps he grew a little bit post-draft.
Somebody like Steve Mason barely played in his draft year. Apparently Columbus' GM pulled an audible and drafted Mason in the 3rd round due to some input from their goalie scout. Leading up to the draft, the other scouts had barely talked about goalies.
Similarly Scott Wedgewood didn't play much as a backup in 2010. Then he had one notable 70+ save playoff game in the OHL playoffs. That alone seemingly vaulted him from being a late round pick to being a 3rd rounder.
To put it shortly, some teams are making decisions on a very limited sample size.
Ryan Miller was a late round pick since he wasn't playing in a notable league. I forget if Jonathan Quick submitted the paperwork to be eligible in 2004, but he didn't get drafted until he was 19.
I would be curious if there was video of Lundqvist from around that time. The butterfly was just becoming the standard by the late 90's. Lundqvist of the late 2000s might look like a completely different guy than him as a teenager in the late 90's. There's some clips from the late 90's drafts and the goalies look so clunky compared to the teenagers today.
As a beer leaguer I can attest on the how much better the pads got between say 1995 to 2005.