He was aware of the concept of pools, and he was aware of the possibility of someone gaining more than 50% of the hashing power:
The incentive may help encourage nodes to stay honest. If a greedy attacker is able to
assemble more CPU power than all the honest nodes, he would have to choose between using it
to defraud people by stealing back his payments, or using it to generate new coins. He ought to
find it more profitable to play by the rules, such rules that favour him with more new coins than
everyone else combined, than to undermine the system and the validity of his own wealth.
I suspect that the concept of a pool acquiring more than 50% of the hashing power didn't go over his head. It's clear that he expected the financial incentives to protect the network regardless. At least with a pool, the people leasing their hash power to the pool can choose to leave. That makes a pool with more than 50% far more secure than Satoshi assumed a lone individual with more than 50% would be.
He wasn't aware of pools when he designed bitcoin and laid the foundations of the protocol. It wasn't till much later when bitcoin was already well established that pools went from theory to reality. Pools were invented to solve the problem of variance in mining as I'm sure you're aware. But variance was never a major issue in 2009 and thus there was no problem to be solved.
The problem of centralisation and trust has existed for a long time now. I specifically remember the community having the same outrage over Deepbit having almost half the hashing power on the network
despite Deepbit having fees of 10%.
Ever since the original Deepbit debacle bitcoin has relied on trust being placed in mining pools that hold significant hashing power.
How can bitcoin be described as trustless and decentralised if we rely on a centralised power not to attack the system? I understand that it's not
likely that a mining pool will attempt such an attack, and that it's almost never in their economic interest. However that doesn't negate the fact that the system still
trusts that single actor to act rationally.
Given the the fact that the value of bitcoin still thrives it would seem that the market has decided that this is an acceptable level of trust and centralisation.
But the market accepting a certain level of risk does not change the fact that the risk itself is the risk of trusting a centralised actor. Thus Bitcoin is not a trustless decentralised currency but a pseudo-decentralised one.