Does the Portuguese higher education system follow Humboldt's model? According to the other question on Academia SE, the Polish higher education system closely resembles the German one:

Which country or countries inspired the post-communism Polish higher education system?

Polish higher education follows Humboldt's model so does German education. I personally hate Humboldt's model as it is a time-hog in the case of undergraduate and masters levels.
Does the Portuguese higher education system follow Humbolt's model?
If No, which model do they follow?
Yes, Portugal's basic education system does follow Humboldt's model. In university, it mostly depends on the institution you choose to study on. I don't know what kind of degree you're thinking about pursuing, but investigate the various universities that offer that degree and it's culture / philosophy.