Whether ninjutsu training online can be practical and effective depends on what you're trying to achieve.
Ninjutsu at the highest levels practiced today...
In the Gyokku Ninja Clan, Ninjutsu training in the higher levels equals the training of most special forces, including battle tactics, modern urban warfare, electronic counter-measures, survival in various environments, structural infiltration, and much more. To imply that all this can be learned at home is quite obviously ridiculous.
Equipment
Ninjutsu is also a highly equipment-intensive art. At even intermediate levels, Gyokku Ninja face each other in battle armor in training battles in which they use every possible weapon (padded training weapons) of the ninja - this includes tactical bows with blunted arrows. Yes, in sparring in the Gyokku Ninja Clan, it is acceptable to shoot your opponent down with a blunted arrow from a tactical bow, and he or she must deflect the arrow successfully and close the distance so you cannot use your bow so effectively... or forfeit the round. Without the special training armors that allow such realism in combat, a ninja can hardly attain their full combat effectiveness.
Then there are all the basic, traditional weapons of the Ninja...
A modern ninja also uses camouflage outfits of various types, specific to different environments, weapons harnesses, tactical bows, electronic counter-surveillance equipment, and more.
So what IS possible in online Ninjutsu training?
Quite a lot, actually. If an online ninjutsu training program has been designed around effective self-defense in an urban environment, and if it's been designed to be studied online, it can be especially effective. This would mean that there would be emphasis on striking and attacks on nerves and blood vessels, as these attacks are easier to learn and more effective in urban self-defense than grappling.
You can go to this link - it is an introduction to such an 'self-defense-based' ninjutsu program.