E46's are no more unreliable than any other car.
There are some common failures, which can be mitigated by preventative maintenance.
Most common are coolant failures (expansion tank leaks, water pump failures, etc.) Most of these are considered standard maintenance after 120K km
Also common, especially with colder climates, are CCV/oil separator failures. More common when used on short trips in cold weather (oil doesn't get over 100'C to boil off water buildup, CCV freezes, then valve cover blows. Best fix it to get an oil pan heater and install enhanced cold weather parts.
Other problems are the rear subframe tears, which seems to affect years before 02. This is a big costly repair, which can sometimes be covered by the dealer, but only if the suspension has not been modified.