On other hand 3 confirmations is enough for lower amount of BTCs.
Yes these are the best way of getting your bitcoin transaction most securely. But 6confirmation or 3 confirmations are best suited only with latest bitcoin core client only. If you use old bitcoin-qt client then you must wait for some 30 confirmations.
When pools are SPV mining, they don't check the validity of the block and whether it complies with the network. Those mining pools then generate invalid blocks which get invalidated by Bitcoin core 0.10+ but not anything below or on 0.9.4 or earlier as those Core clients are not aware of the new rules. AFAIK, this isn't a threat right now. Majority of pools are mining on correct rules and creating valid blocks.