I suppose you refer to use access-lists to permit/deny some traffic through your router, not to access-lists used in dynamic NAT.
If it's so, there's no problem at all. I'm managing a Cisco 3640 with dynamic and static NAT and using access-lists to permit/deny some traffic. NAT inside in eth interface and NAT outside in serial interfaces. I don't know if you need specific IOS version to support both NAT & access-lists but I don't think so.
In my case, I put inbound and outbound access-lists in serial interfaces. If you want to do a similar configuration, when you write your access-lists (standard or extended) you must always put inside IP addresses ALREADY NATTED and outside IP addresses NO NATTED, regardless of they are source/destination IP addresses in inbound/outbound access-lists.
Hope this helps