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There is no advantage to using a polarised capacitor. The fact that electrolytic capacitors are polarised is a "disadvantage" (actually trade-off for higher capacitance) which arises from the physical construction of the electrolytic capacitor. An ideal capacitor is not polarised.
I don't see any obvious problem in using all ceramics on an Amiga mobo, but it would be nice to do some ripple measurements before and after with a scope.
Of course one may prefer to replace like-for-like just to retain the original looks of the board.
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