I asked about this at the local GW and they state that more than one relic on a model is fine. One of the GW employees was even painting up a model with the shield eternal and burning blade.
I think in terms of which is better, I'd say in most cases the thunderhammer is better for the points reduction and makes it so the Chapter master isn't as insanely expensive, but it also is really nice to be able to strike at initiative with high strength AP 2.
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