Like Linux itself, most software for Raspbian (a Linux based operating system) is not of a commercial nature.
Its written (or converted to Linux) by volunteers, then distributed (free of charge) through the use of software repositories, and specially tailored for the systems that use these repositories. thats why you can be sure that software in the repository for your system is suitable, tested, and working.
In case of raspbian, someone (some group of people) has re-compiled all the programs in such a repository (the one created for Debian Linux) into code suitable for the ARM CPU used in the raspberry PI, some 15.000 programs, with new ones added daily.
installing software on a linux system is *always* (almost always) done through the use of the linux software installer system, called apt-get (at least when using a "debian based" linux distribution, with Linux there almost always multiple options)).
this means that (with apt-get) you can always update, or un-install such software, as apt-get keeps track of everything.
synaptic is simply a shell, (helping program) to make choosing what to install easier, but its not for NOOBS, that is why many linux systems also have an easy menu system for choosing what you want to install. but behind that menu system the work is done by apt-get.