Value

"A value" is a quantity. Such as: "X has a value of 29." Whereas, value itself could be quantifiable or instrinsic, for example "My life has value to me." Value could refer to its monetary worth, or its personal worth. Value itself may or may not be arbitrary.

Purple Dragon's right. Anything can have value, or have some value; but when it has a value, it's a quantitative measure, and math probably comes into it.

I'll go with the simple objective vs. subjective angle.

'a value' can also leave the door open for a negative total assesment. 'Some value' often works better for this, as in "Bob's a jerk, but he has some value, if only as a bad example!". Speakers might use 'a value' as shorthand, meaning a single positive property was all that existed in a sea of negative value prperties.

"A value" indicates a specific assignment of value.

Without the article "a" it simply means the speaker or writer see value in "it", making it not worthless. No indication of specific worth is implied.

"a value" is defined and tangible
"value" is abstract

To me, "a value" is an extrinsic quality and precise. Value, on the other hand, is intrinsic and vague.

The difference is instantiation.

Simply put, "It has value" is qualitative, as in "valuable".

"It has a value" is NOT quantitative, it's simpler than that: "It has a value" can only be interpreted as "It has a number [associated with it]".

Context is absent, but I'd say, "It has value" means "It is valuable." Meaning: substantial value.

"It has a value" means "It is not worthless." Meaning: minimal value.