The section "A Clear Path to the Target", on page 205 of the PHB states "To target something, you must have a clear path to it, so it can’t be behind total cover."

The spell Scrying, contains the following text:
"You can see and hear a particular creature you choose that is on the same plane of existence as you. The target must make a Wisdom saving throw, which is modified by how well you know the target and the sort of physical connection you have to it. If a target knows you're casting this spell, it can fail the saving throw voluntarily if it wants to be observed."

Additionally, it says: "Instead of targeting a creature, you can choose a location you have seen before as the target of this spell. When you do, the sensor appears at that location and doesn't move. "

So, by RAW, does this mean that you can't target a creature or location that you can't already see/ is behind total cover from you? This seems to make the spell entirely useless, along with most spells that are commonly used for spying or long-range communication.

Personally, as a DM I am tempted to just throw out this entire section, it doesn't really add anything and I doubt it's worth the headache or ruining large parts of the game. However, I would like to figure out the RAW just so I know what I'm overriding, if at all. Am I missing something or is Scrying basically useless?

Technically, yes, the spell might be nearly useless; but nobody would rule that way

The rules on "A Clear Path to the Target" state:

To target something, you must have a clear path to it, so it can't be behind total cover...

You are correct that if the creature being spied on by scrying counts as a target then the rule above would mean that they cannot be behind total cover. However, whether or not that creature counts as a target of scrying is up to your GM.

We have now run into the nearly unsolvable problem of "What counts as a target for a spell". As my answer there explains, assuming that something is a target whenever a spell's description says so does not end up working. In the end, it would be up to a GM to define the term and decide what counts as a target of the scrying spell (or any spell).

If a GM really ruled that the "target" mentioned in the spell's description counts as a target for the spell and is then subject to the "A Clear Path to the Target" rule, this would indeed make the spell nearly useless. This shows that these rules are not meant to be used to come to this conclusion.

The range of Scrying is "self", so the caster targets him/herself first

The spellcasting rules says that the target must be withing range:

The target of a spell must be within the spell's range

However, range of Scrying is "self", so initially the caster is targeting self, not the creature he/she is scrying:

Scrying

5th-leveI divination

Casting Time: 10 minutes
Range: Self

You can see and hear a particular creature you choose that is on the same plane of existence as you...

After you target self and cast the spell, the spell effect gives you an ability to "see and hear a particular creature you choose". The "target" mentioned afterwards clearly does not obey the general rules for spellcasting — it has its own specific rules based on the target familiarity.

Furthermore, RAW a clear path to the target is required when the spell affects the target:

A typical spell requires you to pick one or more targets to be affected by the spell's magic. A spell's description tells you whether the spell targets creatures, objects, or a point of origin for an area of effect

The Scrying spell does not affect the target, it "creates a sensor", it's another reason why this rule does not apply:

the spell creates an invisible sensor within 10 feet of the target

In the scrying spell the line

"You can see and hear a particular creature you choose that is on the
same plane of existence as you."

gives you the range. You can use the spell on any creature, anywhere on that plane, as long as it is the same plane as you are currently on.
The use of the word target is simply used to designate the creature you are making the subject of the spell. It is incorrect to think that the same restrictions for a combat target apply. One is a noun 'the target', the other is a verb 'to target'.
As intended the spell is meant to be allow remote viewing of a creature or place that you know of in some way. The spell is most definitely not useless.

Here's another example from the Sending spell:

You can send the message across any distance and even to other planes
of existence, but if the target is on a different plane than you,
there is a 5 percent chance that the message doesn’t arrive.

Clearly, in this case, even though the word target is used, the spell is not intended to blocked by line of sight or cover.

This is probably a case where a specific rule (for how you select Scrying's target) overrides a general rule (that you must be able to see your spell's targets). The spell has rules about the target, and for it to be of any value to the caster, those rules must replace the normal targeting rules. It's useless to scry on somebody you can already see after all!

Alas, the writers of 5e spells are not always consistent when something related to a spell as a target and they seldom call out when a spell's specific rules override the general targeting rules. So, as in all unclear situations, the DM at your table will probably need to make a ruling on how it works for your game. I think that for Scrying it will be fairly easy for them to say you don't need to see a creature or location target (since becoming able to see around them is the whole point of the spell), but for other spells there may be more than one reasonable interpretation.

It may be worth while for the players of spellcasting characters to ask their DM for interpretations of spells before they pick them for their characters. If an unusual situation comes up with a new spell and the player and DM haven't discussed it in advance, it may make sense for the player to be allowed to pick a different spell if the DM rules that it works differently than the player expected.