Unfortunately this one is a big "it depends".
Each type of unit has its advantages. Trukk boyz can make it across the table very quickly - in some cases even fast enough to pull off a first-turn charge, but at any rate much faster than a unit of boyz on foot. Trukks have two big disadvantages to keep in mind, though. First, they're the most flimsy transport in the game. AV10 can be popped by massed bolter fire, or dealt with easily with support weapons, and true anti-tank weapons will make mincemeat of it.
All too often, that means your canny opponents will concentrate their anti-tank fire on your trukk(s) early in the battle, often before your first turn, and slag them. If you're lucky they'll merely be immobilized or get a kareen/krunch result, and your 12-ork unit will have to foot-slog it anyway; if you're unlucky it'll go off like a bomb in the middle of your formation and do a bunch of wounds to the riders and surrounding units. There are no defensive upgrades you can take that will make this result less likely, unless you have a friendly Big Mek with Kustom Force Field nearby. (But a trukk is generally too wimpy a transport to devote to moving your KFF Mek around!) And unlike Dark Eldar skimmer transports, you can't turbo-boost for a cover save. To a degree, you might be able to drive into cover or out of lines of sight, but that will slow down your trukks...
The second problem is the transport capacity. 12 regular ork boyz don't really have a lot of staying power. Taking even a few wounds will knock them out of fearless (and taking a lot will mean you either run when you break, or No Retreat will kill most of the unit off!) They'll work fine against light units like artillery, against combat-squadded Marines (that aren't assault marines!), and for knocking out a key vehicle or two. But a bigger squad can be a lot more potent.
Footslogging isn't necessarily the answer, though. Orks aren't fast, they can get hung up in terrain, and they're a really attractive target for blast weapons. Furthermore, it can be bloody hard to maneuver a unit that big around ruins, blocking tanks, etc. But eh, at least it's free, and against lists that focus too much on one-shot heavy anti-tank, a lot of footsloggin' boyz will carry the day.
Pretty much the worst thing you can do is only take one trukk. You can safely assume EVERYONE will have enough anti-tank to take out one. Having two or three spreads them out, and if you have a whole lot of vehicles, that increases each trukk's chances of making it through (especially if you also have, say, battlewagons, kans, buggies, and other things which the enemy will be worried about!)
There isn't an obvious "best way". If you're worried about buying units you won't use, then before you stock up, you need to sit down and decide what kind of army list you think you're interested in. Kan wall? Lots of vehicles? Green Tide? Once you're there it's pretty easy.