If we are meant to understand from the Nazir that forbidding things which are really mutar in order to be "extra holy" is really not a positive thing (cf. y.Nedarim 9:1), then of what benefit are humroth (if any)? Or are we simply misunderstanding what a humra actually is as spoken of by Hazal (the same rabbanim who told us the lesson of the Nazir)?
There are different types of Chumrot, as I see it.
Sometimes we (personal or dictated by Chazal) need a fence to keep us away from the actual transgression. This way, if we stumble we hit the fence and don't fall into the pit of sin. This is the fence referred to - and recommended - in the first Mishna in Pirkei Avot.
This is your typical Humra.
An example (dictated by Chazal) would be: not having some people eat meat and others milk at the same table.
An example (personal) would be: not relying on the Eruv in case it's broken.
There's a concept of being holy והייתם קדושים - which includes refraining from doing things that are permitted, in order to reach a higher level of closeness to Hashem.
The concept of Nazir seems like "an example provided by the Torah" of the second concept. And here we learn a lesson - that it's better to learn how to use "everything" in the service of Hashem rather than outlawing them.
Some things - like meat and wine - are needed only in very small quantities in the service of Hashem. But refraining from them completely - in order not to over-indulge - is not the recommended way, as per the lessons of Nazir.
The better way is to learn how to control yourself; that helps you reach a higher level of closeness to Hashem.
The סידור מהרי"ד at the beginning of his explanation on Pirkei Avos compares Humroth to protection around a precious pearl. The more precious the pearl, the more layers of protection it is provided. Similarly, by keeping Humroth, we are showing how precious the Mitzvos are to us.
So Humroth have a purpose, even if they forbid things which are permitted. They have a positive aspect and a negative one, and depending on the circumstances it depends which one is controlling.