I'm guessing that you got here by short cuts. Since it has taken me 3 years and roughly 200 hours of gaming to go from 1st-6th level, I can't imagine what a campaign that legitimately got to level 100 looks like, but I can tell you that it would need to met more than once weekly for 8 hours at a stretch since the beginning of 3e 13 or so years ago. 6000+ hours of gaming? I just can't fathom it.
Incorrect. Different people use different XP charts, and additionally, different people use different amounts of combat, story awards, etc. to advance PCs. There's also the rule that limits XP gain beyond what it takes to advance a level, until you actually do advance, which was a hol;dover from 2nd Edition IIRC; if you have a level-training rule (which a lot of GMs do, to slow down PC advancement), then it becomes quite possible to lose XP to that rule because the PCs simply don't get back to town and trainers quickly enough.
I ran a game that started in 2001 under 3.0 rules, transitioned to 3.5 later, and had to use the Immortals Handbook when it came out (yes, it wasn't vaporware, though you could be forgiven for thinking that it was since it took forever to arrive and wasn't widely advertised or used) because the PCs actually were Just That Powerful by then. We essentially ended mortal-level gaming around 40th level, and transitioned the PCs to deities and kept going in Immortal territory; that happened back in and around 2008 (there was actually about a year of gaming where all we did was have PCs figure out how to ascend to divinity and Go For It). That game continued until 2010 and did involve "shortcuts" in terms of class levels and HD, since by then what really mattered was Divine Rank of course. During all this time, it was run as weekly sessions of 6 hours each, every Saturday, with occasional breaks for vacations and periods when I personally needed to recharge my batteries. Most of the gaming stretch was actually 2 different games (with different PCs in each, though often one or more players would have characters in both) run in the same world, so 12 hours of gaming each Saturday more or less.
But based on that experience, and particularly the experience of that initial game and the multiple side-games I ran during the same periods, I'd say that taking 3 years/200 hours to go from 1st-6th level is pretty slow. Each game where I had PCs start at 1 and go from there, they gained their first few levels quite quickly, and the two that didn't end in a TPK after a few levels got to Raise Dead territory after about 6 months. That'd translate to roughly 144 hours for 9 levels.
To the OP's question, I can say that level 100 PCs are pretty damn difficult to challenge, but it also sort of depends on what rules you're using for level 100- there are many ways to go with it. Nevertheless, it is possible- you just have to think big enough. Creatures like the Nexus Dragon, Neutronium Golem, and others can provide legitimately scary monsters, but the best opponents are NPCs built using the same rules the PCs are using- which means it takes a lot of work. Celebrim and other posters who have answered something besides "don't do it" are on the right track: think Cosmic. Think Infinity Gauntlet and Living Tribunal type stuff. Think direct alteration to the multiverse, or even travel to other multiverses (I used that one). Think as big as you can, and then try to stretch yourself to think bigger.
Epic games provide the best stories and most drama possible to obtain in this genre of gaming- don't let the naysayers fool you. But also don't fool yourself- it takes great attention to detail and a flair for large numbers and math to do it well. If you can, you'll have a gaming experience that you and your players will never forget, but most people don't have the patience and attention to detail necessary to pull it off successfully. That is the real reason why most games stop at low levels, assuming the players can stay together to keep it going- it's because running the game starts to become too much work for the GM, and he/she just can't handle it anymore. But it can be done.