Routers don't do tcp congestion control, even when doing nat. If they did, it would cause unwanted state interactions at each router - just think about tcp slow start happening at every hop! The way any tcp stream reacted would depend on how many routers the packets went thru - the internet would simply not work. Then there's all the cpu cycles you'd need to run the tcp algorithms and all the ram to handle millions of tcp states. That's not what routers do.
For the record, I think Tomato is great, very easy to use - I'm using it right now to send this. I'm just telling you guys that enabling vegas will only affect connections to and from the router - NOT connections that are routed thru, even if you're using netfilter and conntract (which is how tomato does nat).
If you don't believe me, download the linux source and look for yourself.
grep for these fuctions: cong_avoid tcp_rcv_established tcp_v4_do_rcv backlog_rcv ucopy.prequeue sk_receive_skb netif_rx
in these files: net/netfilter/*.c net/ipv4/netfilter/*.c
tcp_vegas_cong_avoid() never gets called by netfilter!