Hacking is permanent. Three things add to Hacking: Ship Hacking (to select one of three ships from an ARS), Knowledege Hacking (to get Knowledge from an AI controlled system), and activating a Super Terminal (to reduce AIP). So each time you do one of those things, they will all get more punishing for the rest of the game. So pick wisely, and ideally don't do anything that requires hacking unless you have to, so that you keep your options open. Some general tips:
Ship Hacking: Check out each ARS with a Science Lab to determine if you even want to use hacking. The left-most ship on the ARS tab is the one you get without hacking. So if you want that one, don't hack that ARS. Unless you don't think you need hacking for anything else, I wouldn't bother hacking if one of the alternate choices isn't clearly better for your game. NOTE: In a multi-player game, each player gets to pick a ship type, so you can pick different ships (or the same). This makes Ship Hacking fairly attractive.
Knowledge Hacking: This is meant as a method of breaking you out of a problem spot. If you've spend all your Knowledge and can't proceed, you can use Knowledge hacking to get enough to open a new toy that can break the stalemate. So reserve this only for those times when you can't figure out any other way to get past something. A related point is to not spend Knowledge too quickly. Knowledge lets you beat the stuff the AI throws, so spending it before you see what you need is an easy way to get yourself stuck. Hopefully you won't need to do this more than twice. And never Knowledge Hack a planet you are going to take later...you gain Hacking for Knowledge you could have gotten for free.
Super Terminal: Scouting early will let you know if this is even an option. Sometimes it just isn't worth the effort. If you are playing a high AIP game (taking a lot of planets) then a Super Terminal is very useful. But only if you can avoid Ship Hacking and Knowledge Hacking. You might be able to sneak one Knowledge or Ship Hack in and still use a Super Terminal, but that can be risky.