Wow...I never really saw this thread until now. I don't have the online versions of the "story collection" comics, but I am pretty sure that these story collection comics do not have full SpongeBob Comics issues in them, just select comics from some issues. For example, the description on the second SpongeBob comics story collection, Aquatic Adventurers Unite, (taken from the SpongeBob Wiki) states:
Who lives in a pineapple under the sea? SpongeBob SquarePants! SpongeBob Comics: Aquatic Adventurers, Unite! is a collection of previously published material specially curated by SpongeBob creator Stephen Hillenburg and some of the biggest names in comics. Aquatic Adventurers, Unite! features stories with a superhero theme. The book brings together the main characters and the rest of the undersea cast that fans know and love—all in an exciting new comic book adventure.
The collection "features stories with a superhero theme", meaning that there will be comics from different comic books. Another example is the third collection book, Tales From The Haunted Deep, with its description below:
SpongeBob Comics: Tales from the Haunted Pineapple is the third collection of previously published material specially curated by SpongeBob creator Stephen Hillenburg. Tales from the Haunted Pineapple includes more than 15 short, self-contained stories by some of the biggest comics creators in the industry. These original stories feature all the fan favorites—from Patrick and Squidward to Sandy and Mr. Krabs—in original adventures you won’t see on television. Best of all, this book includes stories with spooky themes just in time for Halloween.
This collection features "all the fan favorites", which means that this collection also will not have full issues in them, instead select comics and comic strips from different issues.
There are four SpongeBob comics collected books. "Silly Sea Stories", "Aquatic Adventurers, Unite!" and "Tales from the Haunted Pineapple" are compilations of various stories. The "Treasure Chest" is also a compilation of various stories, but it also features exclusives pinup artworks, a bonus facsimile reprint of the first SpongeBob Comics issue, and an introduction by Stephen Hillenburg.
There are also two old compilations of some comics straight from Nick Magazine, "Comic Crazy!" and "Comic Crazy: Take 2".
Unfortunately, there are not any full issues collected book.