The short answer is yes.
The long answer involves asking what you mean by 'seeding'. That term gets used a lot in the hobby and I'm not sure people think through exactly what they mean when they use that term. "Seed what?", is the question.
If you're talking about seeding from a bacterial point of view, there's really no point in taking that risk for what at best would be a one or two day change in the length of a cycle. The bacteria that process nitrogen waste will colonize available surface area so long as there is a nitrogen fuel source - regardless of what you do - so 'seeding' your tank with live rock doesn't do anything except maybe speed the process up the teeniest tiniest little bit. True nitrifiers reproduce very slowly from a bacterial point of view, one division every 12-24 hours depending on conditions I think, so let's say you add a small piece of 'live' rock to a 100 gallon system with 100 pounds of sterile rock - it's still going to take days to weeks for there to be enough bacteria on all of those rocks to efficiently process 2ppm ammonia (The ammonia concentration you should aim for when cycling a tank) in a volume of water that large. Adding that piece of live rock will shave what, 3 or 4 days off the process? In the lifetime of your tank, is that worth the risk? The more 'live' rock you add relative to the amount of dead rock the bigger an impact it will have on the speed of a cycle, up to and including potentially eliminating any detectable cycle at all, but I think when most people talk about 'seeding' they're usually talking about taking one or two relatively small rocks and putting them in with a huge amount of 'dead' rock. Rock that has been cycled is technically 'live' though the only thing that will be living on it are microscopic bacteria so to your eyes the rock will still look quite dead.
If you're talking about all the other things that lives on live rock that makes it 'live', such as macro algae, coralline, copepods, worms, feather dusters, sponges, etc, etc, etc. Then yes those need to come from somewhere, they won't just appear from the ether. However, it's not necessarily true that you need to get them from other, matured live rock. That's just the easiest way to get them. In that case, whatever life was on that piece of rock will spread through you're relatively sterile system pretty quickly, and if that includes things that might be considered pests, you'll get them. I would argue however, that whether you intentionally 'seed' your system with live rock/sand or not, you will eventually acquire the full compliment of commensal, beneficial organisms that have proven to do well in aquariums. It's no accident that you can look at pretty much any reef aquarium anywhere in the world and find the same species of sponge (pineapple sponge, that white fluffy sponge that grows in dark sumps, etc.), the same species of bristle worms, the same species of copepods & isopods, the same species of feather dusters, the same species of stomatella and vermatid snails, and on and on. There are obviously thousands more varieties of each of those species out in the ocean, and corals and rock have been collected from very diverse regions of the pacific and Caribbean for decades now, so why do we all seem to have the same varieties of beneficial hitchhikers? I think the answer is that some organisms, through whatever accident of evolution, have a set of traits that make them particularly adapted to living in aquariums. They're VERY good at finding their way in to closed systems whether we want them there or not, and reproduce successfully within those parameters. The first frag of an acans you add, or the fist branching LPS, you're probably going to introduce most to all of the species of pods and worms that are normally associated with healthy reef tanks.
The other question I have is what do you mean by 'deep' in the rock? Things like Aiptasia and bubble algae live on the surface of the rock. Their cells might penetrate a few mm below the surface of the rock, but they don't grow roots or anything. If the rock is highly convoluted with lots of crevices and such, it's very likely that they can and will be hiding out there invisible to you until after they're in the tank and have had a chance to grow (and if they've grown big enough for you to see, they've probably already spread), so if that's what you mean by 'deep', then yes, that can and will happen.
Right, that was the long answer. jeez Adam.
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