Your Pencil and iPad will suffer no ill-effects through keeping the Pencil docked with its host iPad for extended periods. It is recommended that you keep a second generation Apple Pencil docked with your iPad whenever it is not being actively used - as doing so will ensure that the Pencil battery is optimally charged - and, importantly, is protected from deep discharge.
An Pencil set-aside, unused and/or uncharged for an extended period, will deplete its battery - leading to irreversible battery damage. As Apple Pencil is sealed for life, if the battery is damaged is fails, the only remedy is replacement of the Pencil itself.
I hope this clarification helpfully answers your question.