If you jack off lets say 2 times a day.... not like I do... Would that have a lasting affect on your hygiene if you took a shower in the mornings?
It's no issue at all. Assuming you clean under your foreskin (if present), all is fine. It means the equipment is working properly, and you can keep doing it twice a day indefinitely.
I would say as long as you wipe the semen off after each ejaculation, including under the foreskin if you are uncut, then there won't be a hygiene problem. However, if you don't, old residual semen can begin to smell a bit funky after a while during the day.