Scene dumpers, like Duplex, usually remove the update and language files (i.g., NBA 2K13: 15GB down to 7GB). Other games require those language files (i.g., LittleBigPlanet 2 uses Japanese dubbed videos and overlays the audio with other language dubs). Some games verify that the files are all there (i.g., Ratchet and Clank: Quest for Booty [E]). Dumpers don't create an ISO because it's not necessary, when a JB folder works already.
A CD will not degrade a laser faster than a DVD. A CD is not as compact as a DVD, so the laser does not have to focus as acutely. A DVD can also have additional layers, whereas a CD does not. Not using the laser will not degrade it, preserving it.
PS1 disc pressing includes data inside the inner ring, that was for anti-piracy. You need a certain optical drive to go toward the center enough to dump the entire disc. PS2 doesn't need anything special, and can be dumped easily. (I don't recommend dumping PS1 or PS2, as their disc images can be downloaded with today's internet bandwidths.)
PS3 discs need certain optical drives because they're formatted unlike other Blu-ray media. You can dump it from the PS3's optical drive, or from a Sony-compatible external one. An IRD file reveals where all the files and folders are of the encrypted data. If the dumper program does not automatically decrypt the data, you will need a decryption key that you can get from a CFW PS3. PS3 Disc Dumper does this all automatically, so it's just a matter of getting a compatible drive. Dumping from PS3 is simple, but the laser is old and not as accurate compared to a newer external drive. After the disc is dumped, you can swap any modded files you want, then compile with PS3 ISO Tools.
I've never had my PS3 online, but data stolen could consist of PSN login info, credit card info, other stuff on your system. If you keep the PS3 offline, then your info will not get out, if this is even happening.
When creating an ISO with PS3 ISO TOOLS, I choose 3.55, so that I could use my disc images with any CFW. The program may be old, but it still works.