If those apps open, and you can use them, then you have them. They are optional additions to your OS X system, depending on what you have purchased before, and what Apple offers as downloads. Sometimes the iLife and iWork apps all show up as additional installs (and you don't need to do much more except try them out)
Pages & Numbers are part of the iWork suite, now separated into individual apps.
iMovie is part of the iLife suite, and would likely include some of the other apps, such as Garageband, and iPhoto (on OS X prior to Yosemite, now would be the Photos app)
Those apps that you mentioned might be automatically added to your system. Depends on what you might have downloaded prior to that time, and what you might have as part of your AppleID account.
Are those apps listed in your App Store/Purchased tab?
The most likely answer to your question is that those additional apps don't come with OS X, and thus are not part of a completely clean OS X install. But, if you restored from a Time Machine backup, those apps would be restored to your new install from that Time Machine backup
Does that make sense to you?
Final thought: Restart a couple of times, then run Software Update (check in the Updates tab of your App Store) to check for new downloads/updates that may be offered. Fresh installs tend to bring fresh updates with them... All part of the fun
Sometimes you get surprised by what Apple offers for free, when it's something that you may have thought you had to purchase separately.