No, a ninja wouldn't enter the battlefield as a 4/1 due to Inkfathom Witch's ability.
Inkfathom Witch's ability only affects the creatures on the battlefield that it can when the ability resolves. And doesn't affect any other creature that might enter the battlefield after the ability has resolved.
So if you use Ninjutsu to put a Ninja onto the battlefield, it will enter with power and toughness as defined by the card itself.
Would a ninja enter the battlefield as a 4/1 if I played the inkfathom witch woul the ninja entering the battlefield be a 4/1?
No. You have two choices here. You can activate Infathom Witch's ability before activating Ninja of the Deep Hours ability. In that case, the unblocked creature on the battlefield will be a 4/1, but the ninja will enter as its normal 2/2 since the ability to turn unblocked creatures has already resolved and only affects creatures on the battlefield at that time. Or, you can use Ninja of the Deep Hours ability first which means it will enter as a 2/2. Then, you can activate Inkfathom's ability to turn it into a 4/1.
If you want to return Inkfathom Witch to your hand (and it is unblocked), you could activate Inkfathom's ability, retain priority, and then activate Ninja of the Deep Hours ability by returning Inkfathom Witch to your hand. Then, the ability will resolve and make Ninja a 4/1.
No, a ninja wouldn't enter the battlefield as a 4/1 due to Inkfathom Witch's ability.
Inkfathom Witch's ability only affects the creatures on the battlefield that it can when the ability resolves. And doesn't affect any other creature that might enter the battlefield after the ability has resolved.
So if you use Ninjutsu to put a Ninja onto the battlefield, it will enter with power and toughness as defined by the card itself.
If you want to return Inkfathom Witch to your hand (and it is unblocked), you could activate Inkfathom's ability, retain priority, and then activate Ninja of the Deep Hours ability by returning Inkfathom Witch to your hand. Then, the ability will resolve and make Ninja a 4/1.