averow - Yes, there are substantial numbers of seatainers lost from shipping in the Southern part of the Indian Ocean, due to regular heavy seas and regular stormy conditions.
Quite a numbers of these seatainers have already shown up in Fugro sonar scans, lying on the seabed.
And yes, gaining sufficient proximity to the metallic article being searched for, could possibly be a major problem, particularly where the sea bed is exceptionally rugged and consists of deep canyons and ravines.
There are numerous marine magnetometers available, but many manufacturers and sites are coy (for obvious reasons) about advertising the limitations of their capabilities.
This smaller variety of MM discussed in the link below, advertises "deep water capabilities", plus an interesting range of actual search results - but examination of the specs shows a practical limit of 2750M operating depth.
As the MH370 search zone contains regions of water ranging between 5000M and 6000M, it is obvious that despite the manufacturers claims, it still has serious limitations.
Model G882 Marine Magnetometer
Quite possibly, the greatest limitation in the use of a marine magnetometer is in its coverage width, as compared to the apparently sizeable coverage width of Side-Scan Sonar.
High frequency sonar (e.g., 500kHz) apparently provides high-resolution images, but with a relatively small coverage width (50-100M) of the seabed. Lower frequency systems (e.g. 100kHz) apparently provide larger width coverage (e.g. 500M) of the seabed, but with lower resolution.
I'm presuming Fugro is using LF techniques to try and cover the vast search area required to be covered, within a modest and acceptable time frame - and as a result have to accept lower resolution imaging results, as a trade-off.