The type of HPV that causes warts does not usually cause any type of cancers, so if these black spots are due to HPV, it's very unlikely to turn into anything more serious like cancer.
It could be HPV related, because some warts are flat with a brownish/dark colour however it could be something else like an infection, its difficult to tell. So the best bet would be seeing a specialized doctor
Warts on the outside of the penis can be treated by all the types that treat HPV - cryosurgery, creams, lazer etc. It is up to you and the doctor to decide the best form of treatment. It sounds to me that if they are warts, a cream like aldara would be effective as they are flat, but of course you would have to discuss with the doctor.
Like Amie said, wart causing HPV is almost always low-risk non-cancerous types.
As for darker discoloration of the glans, is this recent? I have a few mole/darker pigmented spots on my glans, that have been there my whole life, but I didn't really notice until I did a full examination of my glans. When I first saw them, I thought they were flat warts, but I remembered that they have always been there, so sometimes panic will make you notice things that have always been there.
But prll, I have a question for you. Did you go to a urologist for treatment of the urethral warts? I recently found out there are smaller growths in my urethra as well, and I'm not sure if i should try to ask my main doctor, or go to my urologist for treatment. Also, how was the process of electrocautry?
Thank you for your answers Amie and Monstermistake. These black spots are recent consistent with the HPV infection. They are freaking me out and I will see my doctor again.
Monstermistake, yes I went to a urologist for the urethral warts because i was in pain and it was always watery down there. When I was passing urine, it would go sideways because of the warts. My dermatologist said that is urologists area so I went to one.
I have read that local anastesia is done for electrocautery of the urethral warts, my urologist used mild total anestesia which was a breeze. Slept for 10 minutes and when i woke up it was already wrapped up. It only burned the first day when passing urine and since then it has been very good. God forbid if I get reoccurance down there, I would like to do it with total anastesia as well.
Hope my answer was satisfactory. wish you all healthy days !