Yes, using a higher-level spell slot results in a higher-level spell.
The rules for casting a spell in a higher-level spell slot state:
When a spellcaster casts a spell using a slot that is of a higher level than the spell, the spell assumes the higher level for that casting. For instance, if Umara casts magic missile using one of her 2nd-level slots, that magic missile is 2nd level. Effectively, the spell expands to fill the slot it is put into.
Some spells, such as magic missile and cure wounds, have more powerful effects when cast at a higher level, as detailed in a spell's description.
This first paragraph make no mention of changes to the spell's effects, so it doesn't matter if the spell's effects change - it still fills a higher slot. The second paragraph indicates that sometimes this upcasting changes the spell's effects.
As outlined in the highest scoring answer of the Q&A Does a Life Cleric casting Goodberry at higher spell levels get more potent Berries?, upcasting goodberry does mean the berries restore more points as a Life Domain cleric, because of the Disciple of Life feature.