This method is a little cheesy as the easiest way to circumvent the minigame is to create a command that will add 999 auto-hack tools to your inventory. Enough to hack every machine in the game.

If you're a purist or just really like pipe puzzles this guide is not for you.

For the rest of you,
Here's the method:

First things first
Make sure you've booted up the game at least once before so that the necessary files are created on your hard drive. If you don't do this you won't be able to find the files we're going to edit

Finding the User.ini File
You'll need to navigate to the folder with the User.ini file in it

Remastered:
C:\Users\YourName\AppData\Roaming\BioshockHD\Bioshock

Original Release:
C:\Users\YourName\AppData\Roaming\Bioshock

Detailed Instructions:
On Windows type %appdata% percent into the search prompt and click it which should bring you to the roaming folder.
Once you're at the roaming folder, navigate to the folder labeled BioshockHD (or just Bioshock for the original release) and then the folder labeled Bioshock

You should now see the User.ini file.

Editing the User.ini File

Here's where the magic happens.

Open the User.ini file with Notepad or your preferred text editor of choice.
Once it's opened scroll down until you see a line labeled [Default]
Beneath there are the game's controls.
For this next part you can use any key you want but for this guide I'll be using NumPad0

Next to NumPad0 (or your preferred key) copy and paste

GiveItem 999 ShockGame.AutoHack

If you've done it right it should look like this:
NumPad0=GiveItem 999 ShockGame.AutoHack

https://images.steamusercontent.com/ugc/59215726158650155/71C004D3FA59AD9E2F86950C506EF081BDDB0F92/?imw=256&&ima=fit&impolicy=Letterbox&imcolor=%23000000&letterbox=false

Now save the file, go to properties and set the file attributes to "read only" so your changes aren't reverted.

The Results

If you've followed my instructions you can now boot up the game and at any time press NumPad0 to give yourself 999 auto-hack tools.

https://images.steamusercontent.com/ugc/59215726158457595/7989B2C6BCAF1F71CCFED5FD23FA43C1EEF0CB97/?imw=256&&ima=fit&impolicy=Letterbox&imcolor=%23000000&letterbox=false

Congratulations! Now you'll never have to see another pipe puzzle again!

Thank you for reading my guide.