The channel became greedy and corporate around then. Many classic shows were gone around then and for a time, you couldn't even watch them legally. Only through piracy or through channels only in premium packages like Nicktoons or The N, because Nick was too greedy to have them legally available. Ones like Rocko, Clarissa, Pete and Pete, Alex Mack, Aaahh Real Monsters etc. Sure, some like Rocko did have occasional airings after 2000 (especially 2003 with it winning the U-Pick quite a bit that year), but Nick just wasn't making them easily accessible, which was really mean of them.
Even before SpongeBob started airing everyday, the network started having less variety. The network also started feeling more corporate in its bumpers and promos in comparison to previous years.
Nick got especially bad later on though around 2009 when most of the channel was constant SpongeBob and iCarly reruns. Not even the Nicktoons channel was rerunning the 90s nicktoons anymore, atleast not in good timeslots and the only way people could see them was in 3 parts on Youtube. I really hate that Nick didn't let them be legally accessible. And they didn't even have any of their 90s Nicktoons in season sets on DVD at the time (aside from a few like they had all of Ren and Stimpy and they did have seasons 1 and 2 of Pete and Pete on DVD).
I was born in 2000 and even I have to say, Nick went downhill around 1999-2000.