For the most part, yes. During the course of medication the sperm density increased and malformation of sperm was observed. There is some evidence of dysregulation which does not immediately went back once the treatment stopped. The results are not totally surprising. Terminal elimination of amoxicillin can take days (only the initial elimination follows first order kinetics, then slows down, IIRC). And after that, tissue regeneration will take a while. I am also fairly sure that regardless of which antibiotics you take, liver values will look fairly bad.
You will likely find similar effects with many harsher drug treatments (including other antibiotics) but sperm reduction have also been shown e.g. for aspirin. common painkillers and so on. In animal models, in utero exposure to e.g. acetaminophen and ibuprofen occasionally have been associated with reproductive issues in the newborns.
I think there might be a misconception that drugs are precision instruments that fulfil only a highly specific target. In truth, a treatment involves flooding our bodies with a bioactive component in very high doses that will take care of the acute problem, but will also interact in undesired ways. The term side-effect is a bit of a misnomer as some think it is a minor effect. Rather, every (bio)chemical interaction is an effect, only many are undesired.
This is one of the reasons, why it baffles me why folks panic around vaccination, a short-term treatment with typical long-term benefits, but have no issues of taking drugs, even in the long-term, which is just likely to have health burden. Of course, if there are indications it is necessary to take, them especially as other health effects are more pressing (if you have an ongoing infection, sperm count is likely your least worry).
Just to make it clear- there are no safe drugs that you can eat like candy (and thinking of it, candy has also pretty bad effects on health, including sperm quality and sperm count). We can basically take any drug your are interested in, and if someone looks at it, we will see molecular aberrations that can translate into a variety of phenotypes. Everything has an effect and the baseline of looking at it (as I have said many times) is not whether it is detrimental (because to various degree, virtually everything is, including breathing), but which is less bad.