VBA loop to populate Array

You can't reliably get the Value property of a multi-area range, and if you could then you can't then wrap it in Array() to get an array you can loop over via indexing in a For...Next loop. If you put a watch on your arrays you will see they're likely not as you expect.

Here's one suggestion using a function to transform your table column ranges into an array of values:

Sub populate_table()

    Dim d1, d2, d3, d4, d5
    Dim ttl As Long, x As Long
    Dim i As Long, j As Long, k As Long, f As Long, d As Long
    
    With Sheets("Data").ListObjects("tbl_variables")
        d1 = VisibleCellsArray(.ListColumns("Data1").DataBodyRange) 'see function below
        d2 = VisibleCellsArray(.ListColumns("Data2").DataBodyRange)
        d3 = VisibleCellsArray(.ListColumns("Data3").DataBodyRange)
        d4 = VisibleCellsArray(.ListColumns("Data4").DataBodyRange)
        d5 = VisibleCellsArray(.ListColumns("Data5").DataBodyRange)
    End With
    
    Dim calcarray() As Variant
    ttl = UBound(d1) * UBound(d2) * UBound(d3) * UBound(d4) * UBound(d5)
    ReDim calcarray(1 To ttl, 1 To 5)
    
    x = 1
    For i = 1 To UBound(d1)
        For j = 1 To UBound(d2)
            For k = 1 To UBound(d3)
                For f = 1 To UBound(d4)
                    For d = 1 To UBound(d5)
                            calcarray(x, 1) = d1(i)
                            calcarray(x, 2) = d2(j)
                            calcarray(x, 3) = d3(k)
                            calcarray(x, 4) = d4(f)
                            calcarray(x, 5) = d5(d)
                            x = x + 1
                    Next
                Next
            Next
        Next
    Next
    
    'put on a sheet...
    Sheets("Data").Range("H2").Resize(ttl, 5).Value = calcarray

End Sub

'given a (single-row or -column) range
'  return a 1-based array of the visible cell values
Function VisibleCellsArray(rng As Range)
    Dim rngV As Range, c As Range, rv, i As Long
    Set rngV = rng.SpecialCells(xlCellTypeVisible)
    ReDim rv(1 To rngV.Cells.Count)
    i = 0
    For Each c In rngV.Cells
        i = i + 1
        rv(i) = c.Value
    Next c
    VisibleCellsArray = rv
End Function

Combination Of Table Column Values

Option Explicit

Sub populateTable()
    
    Const wsName As String = "Data"
    Const tblName As String = "tbl_variables"
    Const HeaderDelimiter As String = ","
    Const HeaderList As String = "Data1,Data2,Data3,Data4,Data5"
    Dim wb As Workbook: Set wb = ThisWorkbook
     
    Dim tbl As ListObject
    Set tbl = wb.Worksheets(wsName).ListObjects(tblName)
    
    Dim Data As Variant
    Data = NonEmptyTableColumnsToArray(tbl, HeaderList, HeaderDelimiter)
    
    Dim LowUp() As Long
    LowUp = JaggedLowerUpper(Data)
    
    Dim rUpper As Long: rUpper = UpperFromLowUp(LowUp)
    Dim cUpper As Long: cUpper = UBound(Data) ' or 'UBound(LowUp, 2)'
    Dim Result As Variant: ReDim Result(0 To rUpper, 0 To cUpper)
    
    Dim i As Long, j As Long, k As Long, l As Long, m As Long, n As Long
    
    For i = LowUp(0, 0) To LowUp(1, 0)
        For j = LowUp(0, 1) To LowUp(1, 1)
            For k = LowUp(0, 2) To LowUp(1, 2)
                For l = LowUp(0, 3) To LowUp(1, 3)
                    For m = LowUp(0, 4) To LowUp(1, 4)
                        Result(n, 0) = Data(0)(i)
                        Result(n, 1) = Data(1)(j)
                        Result(n, 2) = Data(2)(k)
                        Result(n, 3) = Data(3)(l)
                        Result(n, 4) = Data(4)(m)
                        n = n + 1
                    Next m
                Next l
            Next k
        Next j
    Next i
    
'    ' Copy to range.
'    With wb.Worksheets(wsName).Range("N2").Resize(, cUpper + 1)
'        .Resize(.Worksheet.Rows.Count - .Row + 1).ClearContents
'        .Resize(rUpper + 1).Value = Result
'    End With
    
End Sub

Function NonEmptyTableColumnsToArray( _
    tbl As ListObject, _
    ByVal HeaderList As String, _
    Optional ByVal Delimiter As String = ",") _
As Variant
    Dim Headers() As String: Headers = Split(HeaderList, ",")
    Dim Data As Variant: ReDim Data(0 To UBound(Headers))
    Dim n As Long
    With tbl
        For n = 0 To UBound(Headers)
            With .ListColumns(Headers(n)).DataBodyRange
                Data(n) = NonEmpty2DToArray(.Value)
            End With
        Next n
    End With
    NonEmptyTableColumnsToArray = Data
End Function

Function NonEmpty2DToArray( _
    Data As Variant) _
As Variant
    If Not IsEmpty(Data) Then
        With CreateObject("System.Collections.ArrayList")
            Dim i As Long
            For i = 1 To UBound(Data)
                If Not IsEmpty(Data(i, 1)) Then
                    .Add Data(i, 1)
                End If
            Next i
            NonEmpty2DToArray = .ToArray
        End With
    End If
End Function

Function JaggedLowerUpper( _
    Jagged As Variant) _
As Variant
    Dim j As Long: j = LBound(Jagged)
    Dim n As Long: n = UBound(Jagged) - j
    Dim Result() As Long: ReDim Result(0 To 1, 0 To n)
    For n = 0 To n
        Result(0, n) = LBound(Jagged(j))
        Result(1, n) = UBound(Jagged(j))
        j = j + 1
    Next n
    JaggedLowerUpper = Result
End Function

Function UpperFromLowUp( _
    LowUp() As Long) _
As Long
    Dim rUpper As Long: rUpper = 1
    Dim n As Long
    For n = 0 To UBound(LowUp, 2)
         rUpper = rUpper * (LowUp(1, n) - LowUp(0, n) + 1)
    Next n
    UpperFromLowUp = rUpper - 1
End Function