For example, take a look at these past relatives of Centropyxis and Leptochlamys from Schmidt et al. 2010 JEM, AOP:
Testate amoebae from 100mya amber in France. The arrow in 1 points to what the authors believe may be fossilised cytoplasm flowing out of the cell. 2) four ventral pores visible. 4-7) holotype of modern Leptochlamys, optical sections. 8-11 potential resting cysts. All scalebars = 20um (Schmidt et al. 2010 JEM)
Curiously, unlike the representatives of modern genera, these amoebae have perforations in their shells. Now, the very resemblence to Centropyxis may well be a case of convergence, as it's not that unusual for an amoeba to evolve a test one way or another - Euglyphids, for example have nothing to do with amoebozoa, and yet have rather elaborate tests as well. But provided these specimens do originate from the same lineage as modern Centropyxis, and provided these perforations are real, and not just holes caused by some predation or fossilisation artefact (their asymmetrical arrangement raises some questions...), it shouldn't be surprising that amoebae have not been in perfect stasis for the last 100 million years (or even more, as is commonly assumed).
On one hand, amoebae are pretty good at what they do, and thus could probably continue surviving well as they are for another few hundred million years. Their large population size should buffer them from excessive drift, and perhaps there isn't as many possible viable ways of being in the 'design space' for an amoeba, though the latter assumption is extremely dangerous and probably very wrong as there seems to be no limit in all the ways those seemingly 'simple' organisms can utterly stun us. But there may be something to it, just combinatorically speaking -- there are more possibilities if you're big and full of junk, like metazoa.
On the other hand, things like amoebae may have had as violent of an evolutionary past as the more famous multicellular creatures. We're not particularly sensitive to variations in structures beyond our familiar scale, especially considering those tend not to fossilise well. So it may well be that a) many of the fossilised modern-looking testate amoebae are actually completely unrelated (if we have issues with morphological classification leading to polyphyly even in modern taxa...!) and b) there have been unimaginable diversity spawned and respawned and extinguished in the past that we simply cannot detect due to the rather crude methods available to us.
What I'm trying to point out is that it is an error to automatically assume that "lower organisms" (*twitch*) are in some sort of long-term evolutionary stasis, as is so commonly done. Of course there are things in stasis, and of course some organisms have had more violent evolutionary histories than others (eg. parasites, especially intracellular ones), but it is probably unwise to predict that based on the 'simplicity' or size of an organism, or, worse yet, how distantly related it is to us. Unless good data supports that, of course --please let me know if such data has been looked at!
Sigh, just as it looks like those of us working with extant organisms have it pretty bad, figuring out even the basic questions becomes so much harder for the paleontologists who only have questionably preserved fragments of the past to look at. It's truly amazing we can even begin to reconstruct any of the past at all! And that is why it drives me furious to hear comments like "We weren't there, so we'll never know what happened in the past, so why should we care?" Personally, I can't figure out what the hell is going on in the present either...
SCHMIDT, A., GIRARD, V., PERRICHOT, V., & SCHÖNBORN, W. (2010). Testate Amoebae from a Cretaceous Forest Floor Microbiocoenosis of France Journal of Eukaryotic Microbiology DOI: 10.1111/j.1550-7408.2010.00471.x