Actually the problem with trackers was they were creating too many requests and overloading the Pokemon servers, which was a direct financial loss for Niantic since they had to add more servers to keep the game playable. Additionally there is the copyright issue - all trackers are getting some advertising revenue on the back of the Pokemon Go game, but I doubt they are paying license fees or anything.
As for Niantic not having a good tracker it is again related to server load and game performance - tracking the relative positions of all nearby mons for millions of players is too intensive. As you might remember there was a pretty decent tracker in the beginning and a map with the location where you caught each pokemon, but those were removed to make the game playable.
Why does Niantic have problems with tracking when other 3rd party programs had relatively no problems tracking Pokémon??
For some time now other 3rd party tracking Pokémon programs have been working relatively well. However, Niantic has not been able to provide it's trainers the same quality of a Pokémon tracking program. Is this because the 3rd party Pokémon tracking programs also have legal ownership to part of their own tracking computer programming? What type of financial damage could the 3rd party Pokémon tracking programs have caused Niantic such that they legally threatened the 3rd party tracking programs to close? Generally legal action has a financial bases when money is lost but if no money is lost there is no damage caused to Niantic. No 3rd party was charging money to use their Pokémon tracking program and Niantic doesn't charge Poke Coins to track Pokémon... Where is there a financial threat and/or loss to Niantic?? What damage has a 3rd party tracking program for Pokémon locations caused Niantic?
Why can't Niantic have the same quality of Pokémon tracking program?? Would Niantic be infringing on those 3rd party tracking programs?
Hope someone can shed some information on this questionable issue.
Answers
"As for Niantic not having a good tracker it is again related to server load and game performance"
No, that's bullshit. They already ping servers for nearby pokemon in a certain area (a ~1km radius I believe). There is no reason why they couldn't just show the exact locations of those pokemon on the map instead of hiding them. It literally doesn't require any extra server capacity to do so.
And on the topic of third-party trackers:
There certainly were trackers that destroyed the server performance (PokeVision for example), but there have been huge safeguards put in place to prevent such abuse. Now each worker(dummy account) is limited to one scan per 10seconds along with soft-bans for workers that move faster than would be physically possible (i.e: scan a place in China, then one in Europe, which would result in a hefty soft-ban).
There have also been trackers that took extremely little server capacity to function. FastPokeMap is the big one. That only scanned an area and then cross-referenced the nearby list with known nearby spawn locations, effectively making it about as demanding as a few real accounts to cover an area of several kilometers.